Neptunia's entire premise is a parody of video games, and revolves around this trope. Every character in the player's party knows they're video game characters, and frequently correct each other on RPG rules, often making references to other popular RPG's. The Fourth Wall is broken constantly, such as during the tutorial, when Neptune comments off-handedly that she has amnesia, so she asks if another character could please explain the game mechanics for the player. During Neptune's ultra-flashy and lengthy transformation, she may even shout, "No attacking while I'm transforming!" In another instance, the character IF gets in an argument with a random NPC, upon which she points out that her stats are much higher than his. Neptune threatens the same NPC, but IF corrects her, saying that while they can argue with him, she's not allowed to kill NPC's who are critical to advancing the story. Even deaths of characters not important to the story are foreshadowed this way, as the characters all point out at one point that that the character that's with them doesn't even have his own animations or artwork, so he is obviously going to die soon. When he does in fact die as they expected, Neptune says she called it.
They take it to such a level that, in an early dungeon, Neptune will complain that it's boring fighting in a dungeon with low-level monsters while having no cool skills yet, upon which another character says every RPG has to start out this way, whether they like it or not, or the game would run out of material too fast.
The girls are so used to doing stuff like this that when Neptune is dropped into an alternate dimension in Victory, her new, more reserved party members occasionally get fed up with her constantly breaking the fourth wall and tell her to stop already.
Mega Man 8 has Dr. Wily's fortress inside an underground lava pit, guarded by a giant robot, protected by an energy barrier, with the first two stages requiring specialized vehicles to even get through before you can get inside. When Mega Man first tried to attack, he was grabbed by the robot and nearly electrocuted to death before he could even get close; it took Duo's intervention to save him. When Mega Man got to Dr. Wily, the old coot paralyzed him with an energy trap and was going to just blast him with a Wave Motion Gun; again, it took Duo to save him and destroy the gun. This is all justified for two reasons: Mega Man tried to kill Dr. Wily at the end of the last game and Dr. Wily had recently gotten a powerful alien energy resource, so he would use the power to keep the little robot far away or go for overkill in case he got to him.
In Super Mario RPG, the Smithy Gang show some astounding competence in their battles with Mario.
At the beginning of the game, Exor the giant sword conquers Bowser's Keep in the name of the Smithy Gang and then promptly collapses the bridge to the Keep to keep "nosy" Mario out of their new stronghold. This leaves Mario unable to enter Bowser's Keep for the majority of the game.
Mack waits for Mario to be busy in Bandit's Way before invading the Mushroom Kingdom, then makes his base of operations in the castle so Mario has to fight his way through the town and castle to find him.
Bowyer doesn't find it fair that the party gangs up on him three-on-one, so he uses a gimmick where he can lock button commands to even the odds a bit, potentially nullifying your ability to use items, normal attacks, or special attacks.
Yaridovich catches on to Mario's travel patterns and heads to Seaside Town, where he imprisons the residents, disguises himself as a Mushroom civilian, and then splits into several copies to make the town appear normal. When Mario arrives, he tells him where the next star is, then holds the real townsfolk hostage to blackmail Mario into giving it to him.
Standard procedure is for Mario to watch any newfound star spin around his head for around six seconds before dropping into his hands. The Axem Rangers snatch the star during his process, leaving Mario to look around confused about what happened before he spots them. Then, aware of what he did to their other comrades, they decide to just run away rather than try and fight him.
Mario & Luigi: Dream Team. You know how throughout the series, Bowser has constantly been used by a higher power to achieve certain ends? He's learned to expect it. Throughout his entire partnership with Antasma, he feigns friendship knowing full well that Antasma simply is using him for his power. As soon as he has everything he wants, he literally chucks the Bat King to the wayside and takes over as the Big Bad, leaving Antasma to get wiped out by Mario & Luigi to tie up loose ends.
Similarly, you know how in most games he quickly captures the princess and Mario and co then figure out how to stop him? Well in this one, he seemingly doesn't, just leaving her to be found by the bros in Driftwood Shore... This turns out to be Kamek in disguise instead of the real Princess Peach. So all Mario and Luigi's work at hiding Peach is for absolutely nothing and Bowser managed to completely throw the bros off his trail for a while, all while having captured the real princess in the earlier cut scene.
Not the mention, he comes dangerously close to derailing any attempt at reaching him. During the bros. attempts to collect the Ultibed Parts, when they find the Jellyfish Sheets in a cave in Driftwood Shores, a trio of Fly Guy Rs suddenly nab the piece before the bros. manage to collect it, with the intent of handing it over to Bowser to keep it permanently out of reach. Keep in mind that the Ultibed is the only means of contacting the Zeekeeper, which is the only being with enough power to destroy the barrier surrounding Neo Bowser's Castle. Had the thieves succeeded in their task, Mario and co. would have absolutely no way to stop Bowser.
Another (very small scale one) happens in the Earthwake battle. You know how usually the player gets to damage/knock back/hurt the boss every turn? Well, this thing seems to have realised how a turn based battle system works, and hence surrounds itself in armour after every other turn. This makes the player have to waste their turn taking out the armour (which makes the boss too heavy to be knocked back) and sets them up perfectly for the boss to use its more deadly attacks on Luigi without them getting the chance to rush the battle and finish the boss off beforehand.
Similarly, in Bowser's giant battle, the player can knock him sideways into the lava for extra damage. Except on every turn after the first one in which this occurs, Bowser gets his army to raise a steel wall alongside the platform, preventing them from using this tactic more than once.
Pretty much the whole plot of Mario & Luigi: Bowser's Inside Story is this. On Fawful's behalf. He engineers a virus called the Blorbs to throw people off his real plan and get them all into one place, then uses Bowser's ego to sell him an item that makes him eat everyone, which gives him all the time in the world to waltz into Bowser and Peach's castles, mind control the population into his army, and conquer the kingdom. Indeed, everything in the story is Fawful being one step ahead of everyone else until the very end.
On the subject of Mario, there's King Boo. After his defeat in Luigi's Mansion, he does not fuck around in Luigi's Mansion: Dark Moon. After shattering the Dark Moon to bring Evershade Valley's ghosts under his control, he captures several of E. Gadd's Toad assistants and Mario when the professor calls him to investigate. When another Spanner in the Works arrives in the form of Luigi, he has Big Boo set up an ambush in the train exhibit to throw him off the trail. When that doesn't work, he rips open a Paranormal Portal to call an army of ghosts to slow him down. And when even that fails and Luigi finds the last piece of the Dark Moon, he pulls Luigi back into his illusion to fight him directly. He does lose the Dark Moon piece, but he knows if that he defeats Luigi, he'll have free reign to shatter the Dark Moon again, as E. Gadd would have no one to stop him. Again, King Boo does not fuck around.
When Jonathan and Charlotte confront Dracula in his throne room at the end of Castlevania: Portrait of Ruin, Death insists on defending his master. Instead, Dracula breaks Mook Chivalry and his own final boss tradition (to Charlotte's surprise) by suggesting that they double-team the opposition. While this doesn't work out in his favor, Charlotte still compliments him for having the idea.
About a century and a half earlier, in Rondo of Blood, Dracula actually sends his forces to attack Richter's hometown in Wallachia. Luckily for Richter, he was out training at the time; when he hears news of his the attack (and abduction of several townswomen), he rushes back; the end result is exactly what you'd expect to happen in a Castlevania game in regards to a Belmont facing the Dark Lord.
Disgaea 3: Absence of Justice, in addition, gives us Mao, who immediately comes up with the following plan to become an Evil Overlord: get his title changed to hero, thereby invoking contractual immortality, kick the current Overlord's ass via Narrative Causality, and simply take the guy's place when it's all over. Unfortunately, the Disgaea world itself is Genre Savvy, and the Hero title is actually turning Mao into a Hero.
Again subverting the trope, Jon Irenicus of the Baldur's Gate series continually rebuffs the protagonist's attempts to find out any information about him — "No, you warrant no villain's exposition from me." Unfortunately, he leaves his journals (in multiple copies, even) and a disaffected Lovable Traitor behind, from which you can piece together his evil plan anyway.
He at least justifies keeping them. Because he had his soul removed, he's suffering from memory problems and keeps the journals as a reminder of what he was doing (or something to that effect).
And there's one point where a careless and unprepared frontal assault on Irenicus simply results in him killing the whole party at once in a way he had prepared based on knowing the protagonist's soul (which he had been pratically dissecting as part of his research) so well. Or something. Before that, he has already made plans to incapacitate the party when they meet, and expects the protagonist to perish as a result of what is in store for them...
His greatest piece of Genre Blindness is expecting the 'perish' part. And when it turns out you don't, he performs a Villain Exit Stage Left and goes on with his Evil Plan, and does not expect you to try to hunt him down for Revengeand for getting your soul back. Which is a bit silly, given the first part of his plan was exactly to expect you to hunt him down for Revenge or for getting Imoen back.
In Grim Fandango, when confronting Big Bad Hector Le Mans, Manny attempts to illustrate his own Genre Savvy. Manny asks if this is the part where Le Mans tells Manny his plans, and he, Manny, proceeds to spell them out in elaborate detail. Responding with a simple "No", Hector shoots Manny, stating that this is the part where he dies painfully.
Rubicante, the elemental archfiend of fire, in Final Fantasy IV is met twice in the game; the first time, he is by himself against your five-man party. Later, he battles your party again. Unfortunately for you, he picked up on the notion of forming a party to defeat a much stronger foe and returns with the other three elemental fiends in tow. At least he's nice enough to restore your party's HP/MP before the battle.
Unfortunately for Rubicante, Gameplay and Story Segregation means that this plays out as a Boss Rush instead of fighting all four fiends simultaneously. There just isn't enough room on the screen for all four of their battle sprites to be displayed at once. That being said, the lineup of the Four Archfiends is arranged so that if one of them goes down before a weakness-targeting spell/ability is thrown their way, the next Archfiend in the rotation will either absorb it and heal themselves or counterattack.
One of his precautions for being the Fiend of Fire is to have an iceproof cloak.
Which ties in nicely to the whole concept of the game: The overrated star who didn't earn his fame (very blatant example during the fetch quest) falls, and the unappreciated support character who's been doing all the real work rises to become the true star.
That's not all. Doviculus exploits Villains Never Lie to say exactly what he has to to create a rift amongst his enemies, turning the united front against him on itself almost instantly. He is happy to allow his enemies to draw the conclusion themselves, rather than feed it to them, so they believe it is their own discovery. He prevents a vital ally of the player from pulling a Heel-Face Turn by killing her outright just after a Hannibal Lecture. And he's smart enough to immediately figure out who his biggest threat is, even when most of the other characters are suffering Contractual Genre Blindness.
However, it immediately vanishes afterwards as Fraaz continues to alternate attacks despite being only vulnerable to the leftover flames/ice of the previous attack while using the attack of the opposite type.
Before that, in The Legend of Zelda: Link's Awakening, there was a miniboss who, at the end of the fight, would exclaim, "Argh! I can't defeat you! I'm outta here!" then would teleport out of his boss arena. Even worse, he raids the treasure chest in the next room, which supposedly held the dungeon's item, and leaves a note in order to taunt Link. But what makes him dangerously genre savvy is that, when you find and beat him again, he flees at the last second again. You have to find him again three times before he decides that running away is hopeless... and puts up a decent fight to the death.
And then what does he do after that? He only gets one third of the Triforce, but figures out that Link and Zelda probably hold them. Thus he waits for the day Link reappears and lets him run around fighting his minions and freeing the Sages, knowing Zelda will eventually reveal herself to him. And when she does, Ganondorf kidnaps her and takes her to his tower, and Link follows, bringing the two remaining Triforce pieces right to his throne room. This guy was good.
Ganondorf does it again in The Legend of Zelda: The Wind Waker, where the King of Evil has learned to rein in his ego and instead spends much of his time working in the shadows, trying to alter the circumstances that led to his imprisonment in the first place. The only serious miscalculation he made was his overreliance on some of his minions. Oh, and a very devastating case of Too Slow.
Yuga in The Legend of Zelda: A Link Between Worlds is surprisngly Genre Savvy for a Smug Snake. Though confident that he managed to defeat Link by turning him into a painting after their fight in the Eastern Palace, he anticipated the slight chance Link might escape and warn Princess Zelda. So he erects a barrier around Hyrule Castle, preventing Zelda and Impa from escaping and preventing Link and anyone from rescuing them. This forces Link to find the other two pendants and obtain the Master Sword to shatter the barrier while buying Yuga plenty of time to hunt for the remaining sages before coming for Zelda and Impa. His only big mistake was not taking Link as a credible threat.
Zoran Lazarevic, the Big Bad of Uncharted 2: Among Thieves is this, at least in situations where Nate is trying to bargain with him. He's clearly been in enough of them that he knows exactly what to do in order to take the bargaining chip away from him. It happens twice:
The first time is when Nate tries to get Lazarevic to release Elena, saying that he will give him the information he seeks in return. Lazarevic simply has Flynn search him. Upon finding the map, he declares: "You have nothing left to bargain with, Mr. Drake." He then leaves and tells Flynn to kill them both, which is actually falling into traditional villain behavior, showing that he is Genre Savvy in some areas but not others.
The second time is near the end of the game, when Nate tries to pull a Put Down Your Gun and Step Away by taking one of his men hostage. Lazarevic simply laughs, gives a grand speech about willpower in which he compares himself to men such as Hitler and Stalin (even calling them "great men"), and then shoots the hostage himself.
However, despite those two instances, he does tend to be Genre Blind in most other situations, especially the one leading to his (very appropriate) Karmic Death.
He actually points out that Nate had killed hundreds of his Mooks in the process of getting face to face with Lazarevic and then questions how someone like Nate can consider him a monster.
The Reapers of Mass Effect are scarily good at what they do. When they aren't performing their genocide, they seal themselves in dark space beyond the galaxy where no one will ever explore to prevent themselves from being punched out. They deliberately leave Lost Technology lying around, knowing that it will be found and used as the basis for all space travel, allowing them to curb stomp every space-faring civilisation. And they made what they knew these civilisations would use as the main political, financial, and military hub of the galaxy, the Citadel, into an enormous mass relay into dark space so when they begin the invasion, they could immediately wipe out the main political structure and military force and disable all other mass relays, leaving the rest of the galaxy easy pickings. The only reason they're not doing that this time around is because of Shepard. S/he's taken all of their options away.
Mass Effect 3 shows that they are well aware of the threat posed by a completely united galaxy, so they do their best to divide and conquer. In particular, they are aware that it is practically inevitable that powerful megalomaniacs will try to reverse-engineer their indoctrination power as a means to dominate them and the rest of the galaxy (Javik said this happened in the last cycle), so they simply let them try, knowing that it will cause said megalomaniacs to fight those who are trying to destroy the Reapers. Also, the Reapers are safe in the knowledge that no organic mind (save for Leviathans), that wouldn't also resist the temptation in the first place, can beat them in a battle of wills, and that it is inevitable that anyone studying indoctrination will eventually fall prey to it.
After conquering a planet and cutting off its military and communications, the Reapers act like it is a war of conquest rather than extermination, and force the conquered governments to come aboard them for "peace talks" (allowing them to be indoctrinated), and thus make the conquered governments help them exterminate their citizens. This tactic backfired big-time against the turians, whose own Genre Savvy let them take the opportunity to smuggle bombs onto the Reapers and take them down in suicide attacks combined with external military action, which become known in-universe as "The Miracle at Palaven".
Sovereign in the first game proves to be this while monologuing at Shepard. At first glance, it appears to be the usual round of Bond Villain Stupidity, with the villain explaining their entire plan to the hero. However, pay attention to what it says; Sovereign is smart enough to lord its superiority over Shepard without actually giving him/her any information that would actually be useful in stopping its plans. It also averts Villains Never Lie by spouting complete gibberish when questioned about Reaper origins and motives. Later, when it came time to attack the Citadel, Sovereign rushed directly into the station, letting the geth fight the fleets circling outside.
The Illusive Man dumped an absurd amount of resources into restoring Shepard from clinical brain death, because he realizes Shepard's Magnetic Hero tendencies would be a Good Thing (tm) to have on his side. Furthermore, he does not want to compromise Shepard's personality by implanting a control module, believing that the qualities displayed in Shepard would be diminished if s/he were firmly under TIM's thumb. That didn't stop him from trying to manipulate Shepard the old fashioned way by filling the crew with sympathetic faces and removing any potential Spanner in the Works with strategic information leaks.
In Ōkami, the final boss grabs and shocks the godly bejeezus out of Amaterasu in the middle of her victory howl. Admittedly, he does nothing to stop it when a Combined Energy Attack brings Ammy back, but he still spends the rest of the fight blocking himself off whenever you try to use the Celestial Brush, which is used for all the most powerful abilities.
In World of Warcraft, one of the dragon bosses, Nefarian, repeatedly yells at his comrades/mooks to kill the healers first, which is always the first rule in PVP combat. If they actually listened to him, it would work; fortunately for the players, they don't.
Foolsss... Kill the one in the dress!
Though Nefarian shows his savvy when talking to his mooks, when you finally fight him in his dragon form, he does notadhere to his own tactic.
The major gimmick of the Nefarian encounter in BWL is that once again, Nefarian is ridiculously genre savvy. He breaks the ranged weapons of Hunters, forces Shamans to drop totems that benefit him, shifts Warriors (including your likely tank) into the old +Damage taken Berserker Stance, roots back-stab happy Rogues in front of his terrifyingly powerful cleaves and breath attacks... some are more effective than others, and the Hunter Call in particular was especially troublesome.
The Dev Team Thinks of Everything too, as when the Death Knight class was added 2 expansions later, Nefarian, by then an overlooked encounter still attuned to classic World of Warcraft level 60 raiders, gained an ability that affected this new class.
And again when the Monk class was added in Mists of Pandaria...
In the Wrath of the Lich King expansion, the Faction Champions heal each other and target the player with the lowest health. It's one of the most chaotic fights in the game.
It should be pointed out though that this particular encounter is specifically modeled upon Arena PVP, with (at least pre-Cataclysm) much different strategy and tactics from other WotLK raid encounters because of this.
Also from WotLK, Big Bad himself, The Lich King, reveals his savvy after looking like an idiot for most of the game. He fights all the players in his throne room, letting them weaken him. When they get close to victory, he kills them all instantly, saying that he needed to know that the PCs were the greatest fighters in the land, because then he can raise them as his undead slaves, and conquer the world. Problem is, he hits Tirion Fordring's Berserk Button, and ends up losing.
Also Arthas' dad, Terenas Menethil, returns from within Frostmourne as a ghost to resurrect everyone, resulting in the entire raid bashing on the Lich King unopposed for the last remaining 10 percent of his life.
Nefarion's back in one of the opening Cataclysm expansion's raids, Blackwing Descent, and said Raid's Heroic Mode could just as easily be called "Dangerously Genre Savvy/Nefarion Is A Gigantic Douchenozzle" mode (for example, adding new adds in one encounter, turning off all the useful side effects of boss abilities in another encounter, improving a boss's attacks in a third encounter)... And then he semi-blows it again with his own Heroic mode fight, where one of his mechanics allows careful players to steal power to make their attacks stronger, hence making it possible to defeat him.
The Omnitron Defense System is the most infuriating example of this. Every time Nefarion interferes, he transforms a major golem attack to have the reverse effect of its normal counterpart. Thus, anyone following the standard survival strategy against those attacks are guaranteed to die or even wipe the raid.
Kerrigan in Starcraft is also an example of this during Brood War and Starcraft II. Once she reasserts control over herself following the death of the Overmind, she often plays her opponents against each other, in order to consolidate her own power base. Almost all of the events of Brood War benefit her somehow, even during the UED campaign. This is taken Up to Eleven in Starcraft II, when she allows Raynor to grab the artifact pieces, knowing that he is going to bring the artifact right to her in order to use it, saving her the trouble of finding the pieces herself.
And she keeps it up in Starcraft II Heart Of The Swarm, despite her promotion of Anti-HeroPlayer Character. She knows she hasn't got much to work with at first and the typical Męlée ŕ Trois would fatally divide her resources, so the very first step of her plan is to eliminate the remaining Protoss in the sector, but leaves the local warp gate, so the other end doesn't realize anything's wrong. It works, and the Protoss don't appear again for the rest of the campaign. She's also very much aware the Terrans have access to technology that can use the Zerg Hive Mind against her. This turns out to be the main reason she kept the Primal, non-Hive Mind Dehaka around. Again, it works like a charm.
The Journeyman Project has Eliot Sinclair, the xenophobic Big Bad, sending three robots back in time to prevent humanity from joining with a friendly alien race. The thing is, he helped invent the original time machine, so he knows exactly how time travel works in this universe. So, he rides to the roof of the player's apartment building long before the past is changed with a sniper rifle. If the plan works, so be it. If it doesn't work, he'll still be on the roof, with a perfect spot to kill the alien delegates...
In one instance in Pokémon XD: Gale of Darkness, Michael (the player character) runs into Wakin of Team Snagem. Rather than engage in a Pokémon Battle, Wakin calls out his Gloom and has it use Sleep Powder - on Michael himself! He then proceeds to jack the kid's Snag Machine while he's out cold. Why in the entire history of the games the other criminal groups don't use this strategy still eludes many of us to this day.
While not a game, the villains in the mangado attack the Trainers directly quite often and are in general seen as much more of a competent threat to the protagonists.
In Pokémon Black and White, Ghetsis is this. He raised his son N to believe that Pokémon and humans need to be separated for the greater good of both. Then he put the kid in command of Team Plasma, a group of fanatics and idealists dedicated to doing exactly that. Why? Because he needed a "hero" to capture the legendary Pokémon with the power to do this so that he could be the only one with Pokémon, which would allow him to take over Unova. And in Pokémon Black 2 and White 2, for the first time in the main videogames, the Big Bad outright tries to harm the player instead of battling him/her to get him/her out of the way once and for all. Not to mention, he creates a device to stop the player from catching Black/White Kyurem, showing that he had learned from his mistakes from the last game.
One of the best examples of this is King K. Rool of Donkey Kong Country fame. He tries to trick the player into leaving or turning the console off by summoning a fake credits roll after you seemingly defeat him the first time.
Nintendo did this again in Zelda: Oracle of Seasons. When you talk to the "sign-loving Subrosian" after having destroyed 100 signposts, the game triggers a fake reset (makes it look like the game reset itself). It then goes back to normal after a few seconds.
LeChuck in Tales of Monkey Island, takes advantage of Guybrush's puzzle solving abilities for his Evil Plan and goes for beating up Guybrush rather than setting up an overtly elaborate trap, and actually kills him when he gets the chance.
In Portal 2, the final boss thinks of everything that you could use against him and stops it from happening. No portal surfaces, start the neurotoxin immediately, bomb shields for him, and bombs for throwing at you. The only reason he loses is because Chell had to reactivate the gel flows in the lower levels, one of which includes Conversion Gel to make portal surfaces... and if he loses, he still manages to trap the Stalemate Button so you can't switch him out with GLaDOS in case he does lose. What finally defeats him is his lack of knowledge of the main ingredient of Conversion Gel.
While explaining every other part of his "Four Part Plan" to Chell, he purposefully left out Step Five.
Earlier, Wheatley makes a big deal about this "big surprise" that's waiting for you if beat all of his test rooms, and then suddenly springs it in the second-to-last room. A trap which hinged around an Aerial Faith Plate, a device that the player had been using and relying on pretty much since the start of the game, managing to trick first time players every time. Even GLaDOS admits that it was a pretty good trap.
You could argue that the Fal'Cie are the most genre savvy villains in the series. Usually, the crystals give the heroes super powers to save the world from the cosmic horror from another dimension. In FFXIII, the Fal'Cie, who I guess ARE crystals, give you super powers to DESTROY the world in order to force the cosmic entity to come back from the other dimension. They take the entire premise of the first few FF games, turn it on its head, and come close to winning because of it. Unfortunately for them, they didn't bank on a second cosmic entity stepping in.
In Dissidia: Final Fantasy, Golbez shows an incredible amount of genre savvy, which he combines with equal parts Magnificent Bastard and Gambit Roulette. He knows that a group of heroes with a dream are bound to overcome obstacles (probably because all of his allies lost to do-gooders with dreams), so he 1) Convinces Kain to buy him time and talks him into talking the Warrior into not messing things up, 2) plants the Wild Rose on Firion/Laguna to get them rolling the whole dream thing, 3) CONVINCES COSMOS to do a heroic sacrifice necessary for the plan to work (and to get God to sympathize with their side), 4) Stalls Ex-Death long enough for Kain to help Lightning and co. seal off the rift, so no more endless horde of monsters can spawn (might have been part of his plan), and 5) Actively encourages the heroes, such as Cecil and the Onion Knight on their quests to get the crystals. Ultimately, no one does more for the heroes to save them than Golbez.
Golbez is nearly rivaled by ExDeath in the same games. Nothing gets past him in the game's plot. He knows arguably as much about the world as, say, Garland does, sees right through the Onion Knight's attempt to flee, and knows that Golbez is a traitor. The only thing stopping him is his sheer apathy towards the whole situation.
In Fallout: New Vegas, the last DLC, Lonesome Road, features Ulysses, the Player's rival. He spends the entire DLC watching the Courier cross the Divide from unreachable safe vantage points and when the confrontation comes, is well aware he'll probably die, so he brings regerating Eyebots that heal him, repair his weapons and armor, and attack you and lets the local pyschopath enemies, the Marked Men, into the arena to make sure that even though he'll probably die, so will the Courier.
He's also clever enough to start the nuke launch before you even enter the final area to confront him, because he expects you'll defeat him one way or the other. That way, his plan to nuke the Long 15 will proceed without him. By Talking the Monster to Death, he's even around to lampshade that particular piece of savvy planning directly afterwards, even as he helps you foil it.
The AI in Awakening took another level in this trope. During missions where you have to protect a defenseless NPC, the enemy will completely ignore your units and zero in on the NPC if you leave them an opening to do so, instead of targeting the nearest unit (and thus probably walking right into a blockade) like in past games.
And besides the AI, some of the enemy Characters are Dangerously Genre Savvy in the story, most notably Arvis in Genealogy of the Holy War, who knows Sigurd is a threat — and plans one of the more diabolical schemes ever concocted to eliminate him without an open fight, where he'd lose: pretend that he's still his ally and then lure him to Barhalla, where after showing him his new wife (who's actually Sigurd's lost and now mindwiped wife Deirdre), he burns Sigurd to death and has his royal mages decimate Sigurd's army.
Also Henry from Fire Emblem Awakening. He's a teenage Blood Knight who joins the heroes's sides... because he figures that, if he does, he will get to fight in the best war ever. And he's right.
In Lunar: Silver Star Harmony, Ghaleon actually demonstrates some of this in the final fight. Instead of randomly picking a target or going for the person closest to him, who does he go for first? He goes right for Jessica or uses powerful attacks that hit everybody, and then picks on a low-health target like Nash or Mia while you're licking your wounds the next turn.
Barbatos in Tales of Destiny 2 is actually this when you fight him. He is well aware that in Destiny 2, Magic is actually the best way to deal damage, so he starts countering magic attacks used against him. He also punishes you for healing, avoids getting surrounded by throwing characters who get behind him back in front of him, and unleashes his most powerful attack in response to item usage (A trait he's retained in every single one of his appearances). He'll even go so far as to negate the effects of the damage reducing All-Divide item and boost his attack power instead.
And in the Tales of Destiny remake, what happens if you set all the battles to "Auto" and run around in circles so you can get easy experience without actually beating the game? Eventually, Barbatos shows up and slaughters you. IF you're on the easiest mode? He unleashes OHKOing Beam Spam in an effort to keep you from taking the easy way out.
For that matter, you can probably consider a lot of Artificial Brilliance this trope - sometimes the AI intentionally does smart things, or is programmed to respond to the way the player uses his tactics.
For example, in Star Wars: The Force Unleashed, in some versions, Darth Vader will observe and punish any flaws in your Lightsaber style, as well as adapting to tactics.
In The Godfather 2, many enemy Made Men suffer from Convenient Weakness Placement. Not a certain Mangano, though: he has a fatal allergy to Car Fu. So where does he hide? In a small area surrounded by car-proof concrete barriers, with only a difficult ramp jump allowing cars in, the bastard!
Wily triggers the usual Self-Destruct Mechanism at the end of Rockman 4 Minus Infinity, but he also has an anti-teleportation field preventing Mega Man from just beaming out. Instead, he has to escape the Collapsing Lair on foot (or rather on the Hell Wheel).
In Lost Horizon, Countess von Hagenhild tries to be this, making a point of telling Fenton that unlike others, she won't make the mistake of keeping him alive any longer than necessary. And yet, instead of actually killing him promptly, she instead wastes time telling him that she's going to do it as part of a completely unnecessary villainous monologue - one which even gives Fenton the next piece of the puzzle, to boot.
In Mega Man Zero 4, Weil anticipated the very likelihood that Zero and the Resistance would most likely attempt to derail Operation Ragnarok when they inevitably found out about it, so he deliberately kept the specific details of Operation Ragnarok extremely vague and had the Einherjar warriors commit their own attack patterns in order to distract both the Area Zero citizenry and the Resistance/Zero long enough for him to finish the actual thing behind Operation Ragnarok: the space battle station Ragnarok, which would target Area Zero. In addition, he also restricted access to Ragnarok to the extent that the only one to board Ragnarok is himself, and also put up various cyberspace protections in the event that someone had to infiltrate via that method. It's also implied that he also revived the Einherjar Eight to fight alongside him to delay Zero as he's trying to get at the core. He also merged with the core so that, in the event that Zero somehow managed to get to him, he'd be forced to fight and potentially damage the core, and thus have Zero risk being destroyed by the destruction of the Space Station.
In Star Wars: The Old Republic, the Sith Emperor has a great bit against the Jedi Knight. Knowing the Knight is The Chosen One prophesied to kill him, the Emperor makes a Manchurian Agent of the Knight's own Padawan and possesses the Padawan at the end of Act One, hoping to off the Knight when they're still weak.
Wilson Da Silva from Max Payne 3 is a heroic example. He knows that the villains will kill him if he tries to dig deep into their plot because He Knows Too Much. He also knows that Max is already a known quantity to the villains, one who has been repeatedly targeted by and has repeatedly beaten back their attempts to kill him. So he points Max in the right direction and watches the fireworks.
In thisTeam Fortress 2 comic, Mister Mayor really understands the threat that the Spy poses. When the police had cornered the Scout and Spy in a bank vault, he knew anyone that would get within knife range of the Spy would be as good as dead. So he has both of them locked in the bank vault.
Gray Mann thrives on this; his cunning intelligence allows him to thwart both the Administrator and Saxton Hale.
In Robopon, Dr. Disc's tower has no door for you to enter; the only door is at the very top, on the balcony. He didn't expect you to blow it up.
Dr. Zeke in Robopon 2 is in possession of a time machine. His brother, Dr. Zero, perished in an explosion at the end of the first game. So he goes back in time to save Zero.
Paintbrush Bogs can make the entire screen monochrome, interfering with the color-changing puzzles in their world.
General Tor in Iji, if he manages to charge up his Phantom Hammer to max power. Charging the shot takes a long time, leaving the player plenty of time to duck to try and avoid it. Cue Tor stomping the ground to knock the player into the air and then fire it for a One-Hit Kill.
Lash from Advance Wars is Black Hole's resident Gadgeteer Genius, and it shows big time despite her childish personality. In her first appearance she anticipates Orange Star will assume her units are Flak's and that they'll charge right in assuming he's too dumb to lay a trap. Of course, you waltz right into a trap and are treated to a cruel spike in difficulty compared to the other missions you've done so far. She only gets trickier from there.
Dark Fact from Ys I is apparently weak against silver because it's the only thing that can bypass the protection of his otherwise-invulnerable Cleria cape. So before the end of the game, he snatches up and hoardes in various dungeons under his control every last bit of silver he can get his hands on, from the [[Infinity–1 Sword Silver Armor and Shield (the Silver Sword that finishes the set manages to remain well-hidden enough for him to overlook it) that's eventually used to defeat him, down to harmonicas and bells. When Adol manages to get the aforementioned silver equipment and storms Darm Tower to go after him, he eventually falls into a teleportation trap that lands him in a prison cell inside the tower, while his silver equipment is teleported to random locations around the tower instead.
While Dark Fact leaves equipment that's technically even more powerful than the silver equipment just lying around in Darm Tower, they still can't put a scratch on him. One could theorize that it might have even been an attempt at tricking Adol to using them instead, that might've worked had Reah not warned him about the cape.
Eddie Shrote in the first The Darkness game apparently figures out that Jackie's superpowers are connected to darkness, and by extension, that Jackie will be Weakened by the Light. When he finally confronts Jackie face-to-face, he lures him into an ambush and knocks him unconscious with flash-bang grenades, then sets up a portable floodlight to keep Jackie subdued while interrogating him.
The Brotherhood in the second game are even MORE genre savvy - their entire organization is devoted to the darkness, so they do centuries of research and fight hard with both darkness and light. They use flash-bangs instead of grenades, their support units' primary weapon is a GIANT SEARCHLIGHT, and they're smart enough to WEAR ARMOR. Mostly at the head, because Jackie's an expert marksman. Their body armor is darkness-infused, making it hard to use Jackie's otherwise game-breaking slash-and-grab move. They also sacrifice legions of their mooks so that Jackie is lulled into a false sense of badassery, and then ambush him (bright room with no destroyable lights, shotgun after he kicks the door down, distract him with an iron maiden and then push him into it) while when he's busy doing something that doesn't involve mowing down people. If they weren't insane (they make a LOT of mistakes), they could have pulled it off.
Big BadGod of Evil Melzak in Alundra, and by extension a lot of his followers. He realizes that God Needs Prayer Badly, so not only does he set up an entire religion around himself, but he secretly plagues his followers in Inoa with horrible nightmares to incite fear and get them to keep praying to him. When Alundra arrives with the means to thwart the nightmares, he eventually sets up a scenario to try and trick Alundra into entering a persons' dream, and then have a squad of Murgg break into the person's house and kill him (which will kill Alundra as well, since he dies too if the person who's dreams he's exploring dies.) When he realizes that the spirits of the dead townfolk of Inoa are inspiring Jess to create more weapons for Alundra to use, as well as discovers Sybil's vision of Lutus dying, which leads to the creation of the Holy Sword, he not only has Ronan keep Lutus alive by any means necessary, but eventually also kill Sybil and Jess so that the sword can't be created in the first place. By the end of the game, he also has his Murgg army kidnap one of the mayor's twin sons and put him to sleep, prompting Alundra to enter the other brother's dreams to locate and get to him (since twins are linked by dreams.) This turns out to be a distraction to get Alundra away from Inoa so the Murgg can burn the town to the ground.