In the firstFinal Fantasy, given the randomization of damage, frequency of encounters, and general Nintendo Hardness of that game, pretty much every enemy is a Bat. Especially the 9 billion enemy types that can poison you. Or paralyze you.
None of those hold a candle to the Sorcerers in the first game, which had a random chance to instantly kill you with every attack. Nothing like getting ambushed and losing your entire party before you can even take a turn to make you call them "Goddamned Sorcerers!"
Even worse than the Sorcerers are the Mages, which enjoy starting the battle by barraging you with instant-kill spells. They travel in huge packs, and frequently attack from behind, usually killing off half your party before you can make a move. Oh, and they hang out in the same cave as the Sorcerers. It's a fun place to visit.
In a less battle-oriented sense, the bats are still annoying from a room in the first dungeon to the most pointlessly sprawling caves, little bats move around, often blocking your way. If you're in a slim corridor, the chances of the bat moving right where you were trying to walk around the damn thing become exponentially higher. Get out of my way, you goddamn bat!
Pretty much anything in Final Fantasy II that has ridiculous defense against melee and thus needs spells to defeat it, given one, the way you gain MP in that game requiring planning and forethought to get more; two, the fact that the more you use your spells—yes, they do get more powerful, but they also cost more MP, which is maddening when Fire 5 would be sufficient but you can only cast Fire 10, and artificially keeping their level low while obtaining more MP is ...doable, but requires skilled Sequence Breaking; and three, ethers cost a staggering amount of gil and restore a paltry amount of MP. Combine this with the fact that running away from many enemies ranges from difficult to impossible depending on how lucky you got with agility boosts and the utterly insane random encounter rate in that game and you have a recipe for frustration. Let's not even talk about what happens in Deist, which contains a dungeon FULL of those enemies that you must go through TWICE, all while being fifty country miles away from civilization.
Castle Kasion has giant turtles that are immune to physical attacks, and require level 2 ice magic to be properly dealt with. You can't run from the buggers either, and you're not likely to have that high an MP count at the time, so when you run out, an encounter with a turtle is an instant game over. Goddamned Turtles.
And to add insult to injury, those random encounter Giant Turtles (Adamantoise) are exactly the same as the last real boss (Excluding a little joke boss) you fought. In the last Dungeon. Worse, in the last Dungeon the best way to do damage to them was using an Item from a Chest. You've likely already used it up. Meaning that you have a chance of running into a random encounter stronger than the last boss!
Any of the Parasite type enemies in FFII are Bats, but it's the Giga Parasites that are really Goddamned. First, an explanation of their context: They appear early in the Soul of Rebirth mode, where the player has the ability to save at any time from the menu—but that's their only advantage. The player has, in the Giga-Parasite-phase of the dungeon, half a party that is drastically, horribly underleveled and underequipped for the threat level the enemies pose, an inventory of pretty much zilch, and several floors of dungeon before they reach a safe zone where they can recover. And every enemy—that is not an exaggeration, every single last one of them—is almost impossible to flee from and capable of causing a Total Party Kill. Except for these Giga Parasites, which hit for piddling damage compared to what their Demonic Spiders and Boss in Mook Clothing brethren can do—the catch is that their attacks also drain MP. A lot of MP. They're fast and have low HP, which means that after the first or second round, the fight's over and the player won—but the parasites got in a few hits, and now Minwu has no MP, meaning that the player will have to reset the game anyways, because while Soul Of Rebirth is difficult, Soul of Rebirth without any healing or offensive magic is suicide. Goddamned parasites.
In Final Fantasy IV, we have bats of various types and colors. All of them love a certain move; Bloodthirst. It's not very strong, but it heals the bat, harms one character, and inflicts Sap. And it has an animation that takes about a second to complete. Now factor in the fact that these bats are fast, often get the first move, and can come in groups as small as two, or as many as six. Oh, and when they get a turn, they all go at once. Now imagine getting back-attacked by six of these buggers, and having to sit through their predictable, annoying, overly long attacks while you frantically mash Teleport, Run as fast as you can, or futiley try to summon something big enough to clear them all out in one move. Screw those bats.
Other annoyances are the Evil Dreamers in the Sylph's Cave. They're fast little buggers that can come in groups of up to six and thus all of them generally get the first turn. They have three moves—a weak fire spell, global sleep, and global silence. They like to cast the status spells most often—which have loooooong animations—and even though their spells are weak enough not to connect all that often, after being hit with six of them, the odds of a good percentage of your party being downed are high. So after sitting through that, you get to slooowly get the party back up and slooowly pick them off, as the Evil Dreamers have much more HP than they deserve. You get nothing of value for killing them, either, and when they AREN'T coming in huge packs, it's because they're accompanying the Malboros. This is just so wonderful.
The Sylph's Cave has something even worse: Goddamned Toads. Coming in groups of three to six, and they're just like the Goddamned Bats mentioned above, only they cast the awful Toad spell in place of Bloodthirst, meaning that you'll almost always have to do some magical cleanup after you escape.
The Shinra Mansion in Final Fantasy VII has the nerve to have two different Goddamned Bats in it: Dorky Faces (which do full-party confuse breaths and come in groups of way-too-many), and more typical bats (which are fast and have a bloodsucking move). And if that wasn't bad enough, the basement has its own Demonic Spider called Yin/Yang. Don't you just love the Shinra Mansion?
No love for the frog monsters who can cast the frog status with a basic attack and cast 'frog song' enemy skill which both frogs all party members and casts sleep (thus preventing you from trying to do any damage to them). Prepare to throw your controller at the wall whenever they attack from both sides.
In Final Fantasy IX, for those attempting to level grind by fighting Grand Dragons on Lanar Island, the Gimmie Cat is incredibly annoying. It appears almost as frequently and acts in a way similar to a Friendly Monster (the lack of their unique theme should tip the player off), by asking for a Diamond. If you give it one, it runs away. If you attack it while it's in that mode, it reacts with Comet. You can defeat it by waiting long enough or using a non-damaging command on it (like Steal), and your reward? One EXP point.
Final Fantasy X has several enemies like this, but the most maddening would have to be the Zaurus in the bonus Omega Dungeon. Terrible EXP, insanely high encounter rate, and very high evasion. Thank god they don't actually have wings...
... but there's plenty of in the chocobo race. Apparently, these seagull-like creatures are jealous of their large golden-feathered cousins the chocobo, and will fly like homing missiles directly towards you. This wouldn't be such a big deal if it weren't for the fact that the chocobo is damned hard to steer, and to get the ultimate weapon for your main character you need to avoid hitting these birds AND hit as many balloons as possible. No, these birds can't actually do any damage to you, but they'll probably force you to cause a lot of damage to your PlayStation controller when you throw it in fury trying to get that perfect time in the race.
People often complain about Tonberries being nerfed in Final Fantasy X-2. However, by the point you can meet them, they have more HP than anything you'll fight (Including bosses) for a long time (9999), they can be encountered randomly anywhere in the Mushroom Rock Road, can kill or severely injure your characters in one hit and give terrible EXP rewards. God help you if you see these regularly and you're trying to go for a no-run playthrough.
Final Fantasy XI has some particularly evil examples. First, the three beastmen strongholds are filled with, well, beastmen. While they only detect by sight or sound, you will soon find out that there are plenty of other enemies that detect by the other method of detection, making it a scramble to find a spot without enemies at all, which will be next to none. Then there are the areas in the game with undead, which detect by sound and low HP, the blood-aggro being not only a longer radius than sound detection, but also not being able to be covered by a spell (Unless it heals HP, obviously). Then we have the monsters that detect people casting magic (ninjutsu isn't detected, though), which seems to have the same large radius as blood-aggro. By Chains of Promathia the developers said "screw it" and added monsters that would detect by sight or sound no matter what stealth buff you had on you. Treasures of Aht Urghan actually had it worse by including not only the above examples, but mobs that could detect by Job Abilities, as well as chigoes, which are microscopically small mobs that are hard to see... and can't be targeted outside of fighting them. Arrapago Reef is pretty much a giant middle finger to stealth as a whole. And they actually didn't run out of ideas in Wings of The Goddess, as they added gnats, which aggro dead people. As in players, not undead.
Note we haven't even gotten started on combat. Remember the chigoes? Not only can you not target them at first, but regular attacks and most magic spells are pretty much ineffective. They can, however, get one-shotted by weaponskills or physical attack Job Abilities. Then we have colibri and imps, the former of which can mimic most spells cast on it back immediately, and the latter can detect by sight no matter what, and also regularly silences and disables use of Job Abilities and weaponskills, while casting all sorts of Black Magic, normally of the Area-of-Effect type. This is made up for their stupidly weak defense, but that's a moot point when a party of mid-60s goes up against an 80-81 Heraldic Imp...
Amphipteres are a new addition. Not only are they hard to spot unless you look up all the time(Similar to Yovra, UFO-ish enemies in the last areas of CoP), but they have a special move that has them stop attacking, but also constantly knocks players back a set distance.
Speaking of Whoring, there's also the purple turtles who will constantly spam their special move that inflicts Disable on any unit who use stabbing/slashing weapons like swords, katanas, etc. If you even try to cure Disable, they'll just inflict it again. Oh and it never misses.
Oh god, the Blackwinds in Brightmoon Tor. Just when you think the the AI's dozen free turns are up, they cast a spell that gives protect and Haste to EVERYTHING, tripling the number of turns you have to wait before your first action.
Chocobos. The yellow variety is fairly frequent in the early game, where you can't do jack for damage. They have decent attack, movement of six panels, and can heal themselves and anything surrounding them. The black and red varieties, while unable to heal, have even more amazing mobility (Fly and Ignore Height, respectively), and both have crazy-strong ranged attacks.
Ahriman. The two stronger forms have skills that cost no MP, and can cause instant doom, petrification, and permanent Brave decreasing, which affects the strength of knight swords, katanas, and bare-handed strikes, as well as your counter abilities.
Chemists, who in the late game start wielding guns, which have 100% accuracy, and have a habit of reviving dead enemies seemingly moments after they've been killed. Their massive attack range is even more fearsome if they're lucky enough to have the knight's break skills.
Summoners. Oh dear god. Their most basic summons have the power of level three black magic with the speed of level one black magic, meaning they deal massive damage in a near instant. Furthermore, in almost every battle you fight them in, they're completely out of your effective range, meaning they're pelting you with massive summons before you can even touch them.
Mind Flayers! They use an area of effect attack nearly every turn that confuses your people with a very high success rate.
Archers. You could be forgiven for thinking they're the best ranged class after seeing the way the computer can snipe your characters with impunity with them. The thing is, archers gain more attack range if they're higher up, and the computer will invariably have archers either at or close enough to the very highest point of the map, while your party will begin at ground level.
Final Fantasy Fables: Chocobo's Dungeon: Coeurls get two actions per turn and have special moves that inflict Silence or Halt, but can easily be felled in one or two hits. Elementals take only 1 damage from most attacks and have moderate attack power, but have only 3 or 4 HP maximum and are subject to status effects like most enemies.
Crisis Core is filled with them too. Movers, who talk reduced damage from everything, have huge health, a powerful combo breaking melee and strong electrical spell you can't cancel them out of by hitting. Sahagin, who mainly just jump out of reach to attack you at inopportune moments, Swarms of insects with huge physical defense and insta-death attacks with 100% effectiveness. There's less than a handful of items in the game that can instant death.
Carteaoraptors and Carteaosaurs in Final Fantasy XIII. Just about any enemy with "attacks quickly and relentlessly" listed on its Libra screen qualifies, but these things take the cake, since Carteaoraptors can use 'Courtship Dance' to summon more Carteaosaurs, and if you can't stagger them fast enough they'll summon enemies faster than you can kill them. Which is easier said and done, due to the aforementioned "attacks quickly and relentlessly". To put it briefly, it means they deliver a quick succession of attacks that stunlock you so much you'll be unable to get any commands off. (Sometimes they'll outright knock commands out of your queue) This is particularly bad when you have to deal with, say, 10 of them ganging up on you at once. They're weak and have VERY poor HP, but the fight WILL go on for ages since they just won't let you get commands off. You can remedy this by using Vigilance, but chances are your Synergist will get attacked just as they're casting the spell, every. bloody. time.
On that subject, Microchus are basically the same, but worse. The real problem is that they're a much more durable than you'd expect from a Ridiculously Cute Critter. (they have around 100,000 HP, each) And you have to deal with them while fighting an Ochu. Did I mention he's an Enemy Summonerand can buff them?
Academia 400 AF in Final Fantasy XIII-2teems with enemies that fit under here. It starts with Ghouls, which aren't that bad; sure, the Fight Woosh and results screen take longer than the actual battle, but they're stupidly easy to five-star, which leads to them hemorrhaging extremely useful Potent Orbs. However, a little way through, they get replaced with hordes of Taxim and Nelapsi. Taxims have a lot of health and love to spam Wound, while Nelapsis dodge physical attacks frequently and come in huge swarms. Even worse, they have huge aggro radii, and Academia is loaded with tight corridors and dead-ends, so you can't even run away from them. And unlike their cousins, they don't drop anything useful, just lousy Vendor Trash. Zubat has nothing on these guys.