Alt Itis: Given that there's nine or twelve classes, depending on the version, and ten different section IDs to go through, it's almost unheard of for someone to only have a single character.
Complacent Gaming Syndrome: You will rarely find anyone doing anything other than playing the Boss Rush quest "Towards the Future" over and over again, as it's the fastest way to gain experience, and the easiest way to farm a particular boss for their rare drop.
By the same token, if you happen to be hunting a very rare item, get used to playing the one quest that spawns the most enemies it drops off of over and over and over and over...
Crowning Music of Awesome: Sonic Team is behind this game, so it's a given. Not only that, but an unofficial "Premium Edition" for Part 2's soundtrack was done by some of the biggest musicians in video game music because it was that awesome.
Ob Lillies. They spawn in large numbers and spit an instant death spell. Oh, and they use an undodgeable paralysis area attack when damaged.
Sinnows, of all flavours. Combined strong attacks with buffs, heal spells, Teleport Spam, invisibility, and/or freeze attacks. Even worse, thanks to their hideously damaging leap attacks, Forces and Rangers can't fight them effectively at range.
Garanz/Baranz: Basically Macross Missile Massacre in enemy form. When playing online, without the benefit of Mercy Invincibility, every attack from these things is basically an undodgeable One-Hit Kill. Facing two in a single room virtually requires someone in the party who can freeze; three or more virtually guarantees at least one player death and at least a 50% chance of a total party kill. Arguably the most dangerous enemy in the game (online, at least...)
Chaos Bringer/Dark Bringer: Lots of HP, hard-hitting attacks, a brutal charge attack, and reacts to being hit by draining your TP, then using it to blast you with a horribly strong ranged attack.
Indi Belras: Fast, hard-hitting ranged attacks with unlimited range, immunity to flinching, and the ability to paralyze in close.
All of the Episode II mini-bosses to a degree, but the Mericarol/Merickle/Mericius enemies take the cake. At range they spit out an unblockable One-Hit Kill orb (and, unlike other One-Hit Kill methods in the series, it isn't based on Dark tech, so raising EDK does nothing). In close it would swipe at you with its claws and if you hit back, it would unleash anotherOne-Hit Kill attack that took out anything in contact with it. Virtually the only way to kill it without dying involved freezing it.
Ill Gills. They're faster than you, they can root you to the ground, and their scythes will absolutely destroy you (and, of course, they have a One-Hit Kill attack, because why not?)
Morphos: Invincible from the front, shoots a beam that is all but guaranteed to knock the player down and pin them in place
Deldepth: Races around the floor impossibly fast (during which time it's invincible), and will rise up only to spit (say it with me) One-Hit Kill attacks (or toss the occasional freeze bomb).
Fridge Brilliance: In a meta sense: the beta trailer boasted that "[...]the world of Phantasy Star Online lasts for an eternity!", a claim that has held true. Even though the last official server was shut down in 2008, private servers for nearly all releases of the game are still being played to this day.
Fridge Horror: Anyone wounded by a creature with the D-Cell Virus eventually becomes corrupted by Dark Falz and turns into one of his horrific minions, as the Beta-772 logs and both Red Ring Rico and Heathcliff Flowen can attest. De Rol Le even has some tentacles on its back that it uses to inject the virus directly into anything it runs into. The mines show that even robots and other non-organics are not immune. So... what's stopping those injuries from infecting you?
The Spread Needle, which is either one of the most loved or most hated weapons in the game. Which one it is depends on whether or not you had one. As a weapon with the range of a mechgun but with the capability of hitting up to five enemies at once and firing speed of a rifle, it can clear out entire rooms of enemies, even on higher difficulty levels, in absolutely no time at all, and could be used by any non-Force class, even Hunters that had no business wielding one (though this was changed in later versions of the game to allow only Rangers to use it). The reason it's so hated is because the game's experience system would only grant shared experience for a kill if a player actually hit the enemy. Since Spread Needles could (and often did) clear out entire rooms before anyone had even a chance to get a hit off, the result would often be the guy with the Spread Needle getting ALL of the experience. Needless to say, pulling out a Spread Needle is a very good way to make enemies. While it was nerfed for the Gamecube release on (and hard, only being about half as powerful as before), it remains a very dominant weapon.
The Yasminkov 9000M. It's a pair of Mechguns that have the range of a rifle, meaning you can hit an enemy from across the room nine times with a weapon that's still more powerful than most Mechguns.
The Frozen Shooter has a near 100% chance of freezing enemies. As such, even the most dangerous non-boss enemy is rendered completely harmless.
Claws in the Ruins. Not particularly dangerous, but they were difficult to hit thanks to their "floaty" movement and they did an excellent job of getting in the way of attacks meant for more dangerous baddies.
Dark Gunners, also in the Ruins. They had extended periods of invincibility, only interrupted by brief periods of vulnerability, they moved quickly across the room and could hit you from pretty much anywhere with their laser shots. Forces, at least, could reliably take them down with techs.
Gibbons in Episode II. Though generally not dangerous, even in numbers, they could use Gizonde at range, giving them the ability to inflict Shock on players, and their high EVP and movement pattern made them tremendously annoying to hit, especially for meleeists.
Recons in the Seabed. Like Claws, they weren't particularly dangerous, but they did an excellent job of harrying players and taking hits meant for much more dangerous foes. More annoyingly, Recons would endlessly respawn until you destroyed their Recobox, which had a ridiculous amount of HP and could be positioned up on a wall, making it hard to target for ranged attackers and impossible to hit for meleeists (hope you brought along a spare handgun!).
Good Bad Bugs: Going back to town via telepipe and returning respawns monsters instead of storing them. This means that each time you telepipe, monsters with a rare variant have a new chance to be spawned as that rare variant. Farming for certain rare items becomes a lot easier and faster. This only works offline, though.
When telepiping back to the surface, your character would take a moment to spawn and, during that time, you could move very slightly through obstacles. Repeatedly piping back and forth allows the player to slowly inch their way through impassable walls in some quests, accessing areas that were not meant to be present in the final game. One area is filled to the brim with slimes, which is nice because they don't spawn in appreciable numbers anywhere else.
A glitch with Vol Opt (in both his normal to very hard and ultimate versions) renders technique attacks against it's first form to read off the ATP stat instead of MST as intended. This applies to all techs, even ones cast from weapon special attacks and weapons like the Maser Beam and the Power Maser. It's possible to actually spam these attacks fast enough to prevent Vol Op from even attacking in it's first phase making this a big time saver for players in a hurry. This bug makes the normally worthless maser weapons which fire pathetically weak gizondes for their attacks a key weapon for Android rangers when dealing with Vol Opt since this bypasses their non-existent MST stat and uses their ATP instead, which allows them to solo Vol Opt's first phase.
Ultimate difficulty Dark Falz's second phase Rabarta and Rafoie chain attacks gain a element of cheese from speeding up super fast that makes them more hard to avoid than they were on lower difficulty levels. On top of this the Darvants that show up before his first phase and that he spits out in his first phase spawn in threes next to every player a little after these attacks end. If you got frozen by the Rabarta wave version unless you had super high HP you'd get hit by all 3 at once and die and you can't do anything about it, making it a really frustrating attack that can easily end a game run.
Sinow Zoas and Sinow Zeles have a Rabarta freeze attack that they occasionally fire off. Given that they usually spawn in groups and that they have incredibly strong physical attacks, being frozen while they're around is practically a death sentence.
That One Boss: A majority of the bosses are rather tricky, but some stand out:
Episode 1 had De Rol Le, who gives Hunters and Casts hell and has a strong attack that strikes the platform you're on at random in the dark. There's also Vol Opt, who will occasionally raise a series of blue lit pillars from the floor, along with a lone red lit pillar. Landing an initial strike on any of the blue pillars will prompt an immediate and often lethal (or, if you survive, debilitating) attack on the party, and has an array of very strong attacks in his second form. And then there is Dark Falz, whose attack are extremely strong, some being undodgeable.
Dark Falz's third form was a nightmare for android players, particularly HUcasts and HUcaseals. He jumps around the arena, rarely sticking in melee range for long, and flickers between semi-invulnerability (he's still vulnerable to techs - which androids don't have - and weapon specials - which runs off of MST, something Androids don't have) and vulnerability every 5 seconds or so. Since android hunters lack any weapon that has a range longer than a handgun (and aren't particularly accurate with ranged weapons either), this made damaging him extremely difficult. Add into this that Dark Falz is a Marathon Boss and androids have limited capability to heal themselves, and it basically meant that androids often had to be 5-10 levels higher than anyone else before they could solo Falz and move onto the next difficulty.
Episode 3 has the Leukon Knight (whose everchanging stats are rather annoying), Pollux (for the Hunters, constant AP gain, an immunity to weak attacks, and a timed ability where she starts ignoring your weapons to hit you directly), Castor (for the Arkz, very powerful long range attacks, dice roll effects are instant-kill on your monsters 65% of the time, and able to damage you by killing your monsters) & Amplum Umbra (who just throws the rules right out the window).
The Episode II Temple, especially on Ultimate. Not only does it feature a collection of some of the most annoying enemies of Episode I (Ob Lillies, Crimson Assassins, Hildelts, Indi Belras...), it also features weird geography that makes the level itself a royal pain to try and navigate.
The Spaceship from Episode II is a weird example. Not because it's particularly hard, but because there are NO QUESTS offline or online that are primarily set there (even private servers often have little-to-nothing in terms of Spaceship quests). Thus, if you happen to be hunting a seldom-spawning enemy from the Spaceship (like Gran Sorcerers or Baranzs), you have no way of improving your hunt yields; you just have to go through the vanilla level over and over and over and over...