These "one levels" will have you beating up more than the enemies....
Shogun's level in Teenage Mutant Ninja Turtles: The Arcade Game easily counts for this. Not only do you have hordes of different enemies on an extremely long level, but they all know how to work together to make your life a living nightmare. Everything from foot soldiers with every ninja weapon in the book, to tiger statues that come to life and run extremely fast and can time their jumping attacks to counter your jump kicks unless you have perfect timing and take about eight or so hits before they finally go down. After all that, you get to fight Shogun, a ghost ninja who can teleport and has a hatchet that can reach considerably further than your weapons can, meaning that it's extremely dangerous to fight him close up. He also swings his weapon at an angle that can counter your jump kicks if you don't time them well. When he loses about half of his health, his head will fly off and start attacking you independently of his body, meaning you have two problems to deal with, and if you defeat him, you get the privilege of going to the Technodrome where the "real" fun begins.
Roxy Richter's level in the Scott Pilgrim game. Enemies that come in droves, including the superfast, superdamaging Ninja foes. Plus, the recoverry shop doesn't show up until about 2/3 of the way through the level, and Roxy herself, while not quite That One Boss, is no pushover.
The second half of the Katayanagi Twins level. Platform jumping on very small platforms, annoying enemies in droves, and no shop at all.
Full Moon in Castle Crashers. The Black Knights that live there are very powerful and numerous, they're set as Heavy so juggling them is harder, and you don't have a whole lot of room to maneuver.
The fifth level in God Hand, which starts Nintendo Hard, proves to be inexpressably frustrating very quickly. One sequence sees you forced to play a cannon-shooting game in an attempt to sink pirate ships; the more you sink, the less enemies you fight in the Inescapable Ambush following, but due to the lousy controls of that game, good luck sinking any. Oh, and at the end of the level, you fight Demon Elvis, who's so hard that the entire next level is easier. Fun...
There's a worse one, though: Level 7, Stage 2, "The Flying Pyramid". It's a small, self-contained arena. First wave: axe-wielding female Giant Mook, cannon-wearing fat guy, Mook. Second wave: another axe-wielder, a Giant Mook with a sledgehammer, and a knife-carrying skinny guy. Third wave: a mohawked Giant Mook, a regular mook, two axe wielders, and a knife-carrier. Last wave: a Sensei. And there is no checkpoint—if you die at any point, you start over.
Don't forget Death Shudder, which is the point at which most God Hand players give up. God Hand is a game that is all about managing the number of enemies that are fighting you at any given time. So you get through the first part of Death Shudder, which has a couple Kung Fu Mooks (though if you don't approach them in EXACTLY THE RIGHT WAY, you get jumped by a whole boatload of Giant Mooks. You stride on, thinking you've gotten through the worst of it. Not in the slightest. Once you get into the next area, the doors lock behind you, and you're met with: 3 Elite Mooks, 3 Elite Axe Women, an Elite Giant Mook, and Tiger Joe, a boss mook from earlier. Not to mention the fact that they all rush you as soon as you enter the room, and when you kill the Tiger Joe, it spawns a Trident Demon, yet another boss from earlier in the game capable of completely ruining you. Worst part? That Trident Demon is scripted, unlike most of the other demons in the game.
MadWorld gives us the Castle Dungeon. The key to the game's fun factor is offing mooks in all manner of unique, vicious ways. The Dungeon only has one way to kill enemies you haven't seen before (the statue). What's more, much of the level consists of very small rooms and hallways, making it hard to manuever in pitched battle - which you will get into, as the enemies are zombies and gardeners. They'll frequently mob you as you try to battle the Giant Mook Big Long Driller. Oh, as for Mr. Driller, the level's challenge is to shove five candlesticks into him - which can only be done while he's catching his breath, which he only does when wounded or after several attacks. But odds are good you'll get mauled by gardeners on your way to putting the candlestick in his back. Pull all of this off? The boss is Frank. Enjoy!
In Grief Syndrome, a Puella Magi Madoka Magica fangame, H.N. Elly (Kirsten)'s stage is That One Level for many players at various levels of skill. All but four enemies in the stage are Ledge Bats, generally hovering around Bottomless Pits and intermittently electrified floors. Most of them are also Demonic Spiders. (Note that, while falling into a pit is technically only two-thirds as lethal as dying, the character will NOT be invulnerable to attack immediately after the Bottomless Pit Rescue Self-Service is done, giving inadequate time to properly dodge.) Anyways, these Goddamned Bats mostly appear in swarms, which, in addition to the usual problems that come with trying to fight off large numbers of enemies at once, has the effect of making it difficult to see what they're about to do. The swarming is also a problem because enemies (but not the player!) can travel beyond the visible part of the screen; and, since they attack with fast horizontal lunges that cover more than half a screen's length (while the player is often restricted to one screen by Ratchet Scrolling), this often results in taking potentially lethal amounts of damage seemingly out of nowhere. This makes them Wall MasterLedge Bats. And since they lunge so far, you better believe at least ONE of them is going to end up off-screen. You know, other than the the ones that periodically spawn off-screen, immediately fly onto the screen (which, of course, is an attack), and then drop a TV set on you. Also, lunging enemies start dealing Collision Damage as soon as they start to attack, i.e. possibly before you could react to seeing them move, so God help you if you try to move past an enemy when it or one of its brethren, hidden amongst the swarm of enemies and/or by the Obstructive Foreground, decides to attack. Oh, and if you do react quickly enough to dodge, make sure you don't do so by jumping directly into another enemy lunging across the screen. Oh, also try to avoid jumping right into a pit or onto a patch of deadly floor. Remember those?
Like everything else in Grief Syndrome, the enemies in H.N. Elly's stage are Made of Iron at higher difficulties. Even worse because your attacks will knock them out of range (they stay airborne) instead of killing them. They'll then proceed to sneak through the Obstructive Foreground or fly off-screen, and you probably won't see them again until they're flying straight at you.
Spartan-X 2, the Famicom-only sequel to Kung Fu Master, has a part in the final level where you have to ride a platform to your destination. The main difficulty comes from the swarms of green enemies that get dropped onto the platform at certain points in the level. If you try to handle them like regular Kung Fu, you will lose a ton of health in short order, and probably get knocked off the platform to your death. Using the uppercut and finding a way to get behind all the enemies is absolutely essential to survival of the first part. Then after this comes a water segment with charging enemies and a not-too-merciful time limit to get to the final area and the final boss.
The full release of [adult swim] Games' Fist Puncher gives us the Green Line Subway, in which you must protect a pack of fleeing lawyers from some escaped convicts. However, if a single one of them takes a hit from anything, including you, they scream lawsuit and you fail the level. The good news is that the enemies never attack the lawyers. The bad news is that the lawyers are EVERYWHERE, and some are programmed to walk directly into your line of fire. In a game that otherwise encourages you to wreck everything that moves, it's a slow, miserable tightrope-walk.
The Elevated Train level by itself isn't that bad, but the main problem is the level's sidequest, getting more kills than The Dragon. At this point in the game, she basically outclasses you in nearly every level, so outdoing her can be a real pain, but you have to clear this sidequest in order to unlock one of the characters.
The penultimate level, the Airstrip, simply because its arguably the longest level of the game, the enemies are the strongest ones yet, and checkpoints are sparse.