This is a thread to list and discuss games that have are primarily underwater or have significant enough parts underwater to be mentioned. (The inspiration to this thread was Super Mario 64's eel.) The discussion of the mechanics of avatar movement in water is also a point to be discussed. I have become fascinated by the idea of having an an entire Metroid game take place underwater; the underwater parts in Metroid Prime 2 were very tense. I think underwater works better for scares from large floating creatures than having an winged enemy or phantasm attack you. It seems like all the developer are focusing there attention on creating impressive open world cities.

What do you think are the best underwater segments? I keep hearing things about some Wii game that lets you swim around in an ocean [Endless Ocean]. Anyone here play that?

Underwater Games
Ecco the Dolphin [GEN]: Dat dolphin.
Endless Ocean [Wii]: large underwater world to swim around in w/out any real objectives.

Notable underwater segments from other games
Super Mario Bros. [NES]
Alex Kidd in Miracle World [SMS]
TMNT II: The Arcade Game [NES]
MegaMan2 [NES]
Donkey Kong Country [SNES]: Underwater monkeys!
Super Metroid [SNES]: Maridia
Mega Man Legends 2 [PS1]: The Nino ruins
Super Mario 64 [N64]: the eel !! the stage with controllable water rising levels.
The Legend of Zelda: Ocarina of Time [N64]: the water temple.
Metroid Prime 2: Echoes [GC]: first person underwater action. Jump into a tank with deadly shark-like enemies!

The ones I can think of off the top of my head:

Mega Man Legends 2: The Nino ruins are completely underwater. As you'd expect this is a physics heavy area and it can be a bit confusing in how to/when to raise and lower the water. Think the Water Temple in Ocarina only much less annoying. You can fight the boss while submerged or not and that obviously influences the difficulty level.

Croc: Legend of the Gobbos: The underwater sections are probably the worst potions of the game.

Super Metroid: Kind puzzled you didn't mention Maridia at all.

Metroid Fusion: The AQA Sector... which was the worst area in the game IMO.

Mega Man 8: Aqua Man
Mega Man & Bass (which sucks): Pirate Man
Mega Man X: Launch Octopus
Mega Man X2: Bubble Crab (most)
Mega Man X3: Toxic Seahorse (partial)

Mega Man Zero 2: Isn't the archives or some area underwater and you have to dodge electric currents. Really annoying....

OMG... do NOT get me started on the Submerged Temple. The fight with the Alpha Blogg is seriously bugged. For some reason I and many people have a real problem with the dodge maneuver not working during this damn fight. Had to redo this place like a million times until I got lucky.

Don't remember any problems with lock-on controls in Prime 2. I've edited those games into the OP. What is your favorite underwater game? Least favorite? You seem to not enjoy underwater segments.

It's weird though... it's just that fight alone I have trouble with. The rest of the game is fine.

Don't really know off hand. I'll have to look through my games... I'm sure there are more I'm not thinking of.

I honestly wouldn't say that. I think I tend to remember the bad ones more because they stick out when it comes to their respective games. Underwater segments in games are a very tricky thing to get right.

I don't really have a problem with water levels in the DKC's (although Pokey Pipes can be aggravating with its reversed controls) and while I can see how Maridia in Super Metroid can be annoying it doesn't really bug me much.

Edit:

Then there is the old school Tomb Raider games. Water sections were pretty prevalent in those. Tomb Raider III took it a bit too far with the Antarctica section however. There's a really annoying underwater stretch were you have to constantly have to use MediPacks because of the damage you're taking from the cold water.

I seem to recall EVO had some underwater stuff to it.  Man I loved playing that game back in the day.

Two of the games I speedrun have underwater levels - Tiny Toon Adventures and Wacky Races. Mercifully, both are relatively short and unobtrusive. Plucky can blaze through 2-2 in Tiny Toons, while you can hold A and speed through the one in Wacky Races. I hate underwater levels in general.

Also of note are the levels in Alex Kidd in Miracle World. Early on, this was considered the Master System's answer to SMB, so to me the underwater levels drew comparisons to SMB's.

Typing on my phone. Cant post for crap.

How about Deep Fear for the Saturn? I never hear people talk about that one. Kind of an RE clone with the far more interesting premise of being trapped in an underground research facility. Shat voice acting, of course, but OST by Kenji Kawai.

Hunt for Red October for NES is underwater. And terrible.

It's weird to see this topic without anyone mentioning Aquaria.