These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ultimate Supreme Executive Chairman Drek, the Big Bad of the first game. At first he may come off as a humorous villain who is trying to find a home for his people by extreme, if unnecessarily cruel means, but by the end of the game, there is no mistaking him for anything but an unrepentant maniac. To begin with, he is the one who over-polluted his own home planet and got his kind, the Blarg, into this situation. He proudly boasts about it and how he did it on purpose, and that his real motive behind invading and tearing apart planets with machinery, bombs and superlasers to build his new world (with people still on the planets in question) is to make the mother of all money-laundering real-estate scams; he's been paid for every square inch of the new Blarg homeworld, and makes it clear that once the people settle in, he'll repeat the whole polluting and planet looting cycle all over again. Oh, and he almost blew up Ratchet's home planet with a superlaser so he could move his new world into its perfect orbit, and it's implied he also chose Veldin just to spite Ratchet for getting in his way. His Karmic Death (by virtue of Drek accidentally launching himself and his mecha straight onto the new planet, and Ratchet then blowing up said planet with Drek's own superlaser) was well-deserved.
Contested Sequel: There is a minority of fans who discount Deadlocked, Going Mobile, Size Matters, Secret Agent Clank, Quest for Booty and All 4 One as being "real" Ratchet & Clank games, which can become confusing when they insist on referring to the game by numbers (e.g. "the fourth game" could variously apply to Deadlocked, Size Matters or Tools of Destruction depending on whether you're talking to someone who accepts all the games, only the platformers, or only the main console games).
However, all but (probably) Size Matters and Secret Agent Clank are canon, regardless.
And then we've got All-4-One and Full Frontal Assault, due to their gaming style.
Demonic Spiders: The heavily armored, quick, and downright nasty Land Lobsters qualify, unless you throw the wrench.
The Y.E.T.I.s from Going Commando's Planet Grelbin; they spawn from out of nowhere (and in large numbers, to boot), have no concept of Mook Chivalry (often ambushing you in groups of ten or more), and are card-carrying members of the Lightning Bruiser club. You could try running from them, but they love spawning right in your path and often appear around Arctic Leviathans, which must be killed for Moonstones. That leaves killing them, but there are a few problems with that as well: first, very few of your weapons are effective against them, the ones that are either have low ammo clips or have ammo that must be bought at a vendor, and for the weapons that don't, you're thwarted again by the fact that there are very few ammo crates lying around the massive ice field you must traverse. As a result, you'll find yourself making frequent trips back to the vendor (because this game oh-so-conveniently forgot to include the P.D.A. gadget)... which means running headlong back into the Y.E.T.I. mobs you just fled from. Simply put, your only real choices are either to gather Moonstones in quick bursts broken up by Y.E.T.I. maulings or to Ragequit from pure frustration.
Qwark's hideout in Up Your Arsenal features heavily armed catchphrase-spewing Qwark Bots. They deal ludicrous amounts of damage with a very high rate of fire, have more armor than any other enemy of their size, and can even survive after being reduced to nothing but a skeletal torso with one arm, often lurking in this state until you pass the cover they're hiding behind to swipe at you. They also spawn in dense packs.
Surprisingly, Captain Qwark was brought back in the second game solely because of this; the staff was midway through production of Going Commando when they realized they missed the big lug, so they came up with the Behind the Hero cutscenes as a way of sneaking him back in, and then decided to just upgrade him to Big Bad status.
Dr. Nefarious and Lawrence.
Courtney Gears as well (mostly because of her music video), even though she didn't make any more appearances since Deadlocked, but was often mentioned throughout the series. But just look at how much fanart she has on deviantART...
Mr. Zurkon. Being voiced by the actor of Mario from Hotel Mario certainly helps.
"Mr. Zurkon does NOT come in peace."
The Groovitron. It even appeared in Playstation Move Heroes!
Fan Dumb: The sequels, the Future titles in particular, have been known to cause certain fans to spontaneously develop rabies.
Fanon Discontinuity: Deadlocked, Size Matters and Secret Agent Clank. At least the latter two don't appear to be canon. On the Timeline on Ratchetpedia, the two games are considered non-canon, due to a lack of proof on whether or not they are canon.
Fridge Brilliance: Lombax anatomy makes a whole lot of sense considering that they're desert creatures. Big ears act as heatsinks, big feet make it easier to walk on shifting sand, hair length also helps with heat management, and yellow/gray hair shades... must i explain this? Their only trait not suited for desert are big eyes.
It makes sense if they're nocturnal (considering the developer is Insomniac Games) or crepuscular. What doesn't make sense is why those large eyes aren't protected by long eyelashes like a camel. Maybe that's what the caterpillar eyebrows are for?
Remember in Going Commando when Angela kept tripping and falling? It makes sense when you consider that female Lombaxes don't have tails and therefore are probably much less balanced...
Another one that makes sense is Ratchet being sent to Fastoon. It has very similar conditions to Fastoon, the Lombax homeworld, and thus is a logical choice for sending a young Lombax to.
The Mega Supernova (The Harbinger's upgraded form) V99 from Deadlocked. All minor foes are vaporized in one shot, and the bosses take massive damage from it.
A non-Infinity+1 Sword example: The Rift Inducer of Up Your Arsenal, which one-shots all small to medium-sized mooks.
Level it up enough, and you can just sit there while all of the enemies in the area get sucked in and die.
Groovitrons in Tools of Destruction. A 100% effective paralysis effect on any enemy in the game bar two or three, and your New Game+ reward gives you an infinite amount of these. Toxic Swarmers also break bosses in seconds if placed strategically.
Considering each of these had rather expensive ammo and you couldn't find the ammo for them in crates like the rest, this isn't quite so game breaking.
Clank's Time Bombs could be used as these if you knew how to use them the right way. However, if you're playing the hardest parts in hard mode, these become more game fixers than breakers.
The Heavy Bouncer in Going Commando does massive damage when it hits an enemy, splits into a bajillion smaller parts on contact, all of which do equally massive damage, and has an absurdly large ammo clip for a weapon that powerful (25) that's replenished by 4 per ammo crate (buying the ammo is dirt cheap). It's so bad that the final boss can be downed easily with just a few shots from this gun, and its Brutal Bonus Level, the Impossible Challenge, becomes a cakewalk with it. The ammo issue was nerfed in its return in Up Your Arsenal, but the weapon itself is just as powerful, if not even more so. Watch in awe as one shot clears a room of mooks in a matter of seconds!
Good Bad Bugs: Using the Taunter in the Blackwater City hoverboard track for infinite bolts, and all you needed to set it up was the Hologuise. The HD version patched this method out, but fans quickly found a new way to access the track by glitching through a nearby wall with the help of the Decoy Glove.
Harsher in Hindsight: In the first game Ratchet was a Huge Jerk Ass. After playing the future series and finding out that his father had to leave him in veldin for the best its kinda hard to blame him. Keep in mind that he had no friends, was a child and only had a wrench to protect himself.
Hilarious in Hindsight: Qwark's Personal Hygenator ad at the very end of the first game, which claims it can solve painful itching in the nether regions, becomes this in light of Going Commando revealing one of it's side effects is in fact severe irritations and itching in sensitive body areas.
The following exchange (which is already very funny) becomes even funnier if you have played the Secret Agent Clank game:
Clank: I believe there has been a misunderstanding. Secret Agent Clank is merely a fictional character I play on the holo...
Nefarious: LIES! SQUISHY LIIIIIIIEEEEE...*jams*
Also, the vid-comic's narrator's utter disbelief at the concept of "robotic pirate ghosts" takes on a whole new meaning once you encounter some in Quest For Booty.
Let's see... Ratchet's a guy from a backwater place who builds stuff, whose melee weapon of choice is a wrench, and who is a proud proponent of "more gun". After looking at it this way, all those Engineers come off as a bunch of posers.
Nefarious self-identifying as "robot" and his pride of being one become funny if you know that the term originates from the Czech word "robota", which means "work" or "labor". Not so superior after all, are we, Nefarious?
A real life example is that the armor that Ratchet wears throughout A Crack in Time appears to foreshadow TRON: Legacy.
Ho Yay: Ratchet and Clank, and to a lesser extent Ratchet and Qwark.
Ratchet: Okay, I have to ask, what's with the nurse's outfit?
Qwark: All part of my ingenious plan to gain Dr. Nefarious' trust as the lovely nurse Shannon.
Ratchet: Well... White's certainly your color.
Qwark: Oh, you think so? I've always fancied myself a winter.
All 4 One brings us some spectacular Qwark/Nefarious moments as well.
Moral Event Horizon: Surprisingly, Ratchet himself nearly crosses this in the first game, being perfectly willing to leave an abandoned commando for dead on a war-torn planet, as well as become apathetic to Drek destroying other worlds, just because he's become obsessed with getting revenge with Captain Qwark for stabbing him in the back. Fortunately, Clank strongarms him into helping the commando by only agreeing to start his ship if he goes to help him, and Ratchet is still pissed off about the matter. Ratchet eventually puts things in perspective later in the game.
Porting Disaster: The PS3 updates of the first four games, done by novice studio Idol Minds, have various glitches and save errors. Deadlocked probably gets the worst of it.
Seinfeld Is Unfunny: The first game, while still well loved, tends to suffer from this. While it was a groundbreaking platformer for it's day, its graphics are really showing it's age now, and the substantial amount of Early-Installment Weirdness compared to the numerous sequels almost make it feel like a game from a completely different series.
Sequelitis: Surprisingly few claims of this given that, if spin-offs are counted, there have been 12 games in the past 11 years.
That One Boss: The battle against the Thugs 4 Less Leader on Snivelak in Going Commando is this for many people - it's not so much that it's difficult, but it takes forever to go down. Your normal weapons aren't very effective, forcing you to run around the city looking for turrets with which to whittle down his health - all the while shooting down his bombs - before he comes and destroys your turret after a certain amount of time has elapsed. Which is why smart players hide around a corner and kill the Thug Leader with spider/tank bots.
That One Level: Gorda City ruins, on Planet Oltanis in the first game. In one path, you have to circumnavigate a path covered in ice (Why is covered in ice, again?) while being blown about by heavy wind. In the other, you have to make it past droves of some pretty annoying enemies, including one grenade-launching ship that's tough to dodge. Oh, and you can't use your jetpack. Yeah, Clank got randomly struck by lightning. Ratchet makes him sit this one out.
The Hoverboard Races, particularly the second one on Kalebo III.
We also have Planet Grelbin from Going Commando. When you're hunting for crystals, polar bears will pop out from underground and they are TOUGH. They can survive at least one hit from any weapon you use (except the RYNO II), and will take a "bigger than average" percentage of your health if they swipe you. And how about those ice serpents that hide under frozen water, then burst out, take forever to kill, can knock you out quickly and can destroy your Shield Charger in one attack? And if you don't knock out those polar bears, they will chase you as hard as possible-and that is by NO means an exaggeration.
That One Sidequest: In Going Commando there were two huge open areas where, for 100% Completion and bolts, you had to collect a vast number of crystals scattered across the map. They [initially] don't show up on your in-game map, you're constantly being attacked by infinitely-spawning enemies, and scouring every square inch of the map looking for that last crystal you require is not fun... especially the Grelbin icefield, where you're facing the ridiculously-tough Y.E.T.I.s (see That One Level above).
Getting 100% completion in Crack in Time requires you to Score High on a Nintendo Hard mini-game fraught with Stylistic Suck. Plus the downright evil time puzzles required to get the last of the Gold Bolts.
Qwark never really did put up a good fight when he was a villain. Having twice teamed up with Ratchet and Clank, he's even more inept than ever, Gameplay and Story Segregation notwithstanding for players assuming control of Qwark in All 4 One. His glory-hound attitude, if it didn't already piss people off, it will now.
Helga may count. She is mostly saying she can do better than Ratchet on fitness courses, though we don't see her do anything but yap all the time.
Ratchet himself was this in the first game, due to his massive Jerkass personality, and his horrible treatment towards Clank, who was only being nice to him. The second game rewrote his personality, and kept it that way.
Villain Decay: Captain Qwark - in the first game he was one of the two main villains, and he returned as the main villain in Going Commando. He showed up as an early boss in Up Your Arsenal, but from that point on Qwark ceased to be a villain so much as a hindrance because he was so inept at trying to help. By the time the Future series starts, no-one can take him seriously.
What Do You Mean, It's Not for Kids?: The first three games got so many things past the radar, the T rating for them might more than justified despite the cartoon-like look of the game. The developers admitted that the game was made more for the teenage crowd and older rather the younger kids.