Rayman Origins/Legends, Tropical Freeze and NSMB Wii Penguin Suit leap to mind.
TF and Rayman are pretty similar in style, I get the impression that Retro might've been influenced by Rayman Origins water movement what with the spin attack and analogue control. Difference is the weighty factor where DK continues to carry his style of momentum even into the water stages (and also needs air) while Rayman is quick and more easily manoeuvred, both styles fit their respective games.
Legends had more interesting water stages than Origins mind you, I'd say Origins had the swimming down but it didn't have enough ideas to match the number of water stages in it, especially considering the second round of them just repeat the same ideas, for once Legends having less was more.
Penguin Suit is pretty circumstantial but it's the best 2D Mario has controlled underwater, shame that they made it a post game bonus in NSMBU dooming that games water stages to mediocrity for the most part.
Anyway, asking for favourite Water Levels in platformers? I actually tackled this question once before so copy/paste time.
Vanilla Fortress (Super Mario World)
While SMB3 dabbled in having a fort with water in it I can't say I held them in much regard. What makes Vanilla Fortress work so well to me is how its obstacles tend to stick with those only found in castles and forts, the whole stage was waterlogged from start to finish yet the old hazards of Thwomps and spiked balls remained creating a new way to approach these standby hazards. It's also one of the few Mario stages with a split path. Considering the same game has water stages as bafflingly bare as Star Road 2 it sort of helps this fortress standout further, it's also not as tightly tunnelled in as other water stages in the game, basically I think it hits a lot of the right notes.
In fact to this day I get excited when a NSMB game brings out a watery fort or tower.
Mondo is also pretty cool for a water stage.
Hydrocity Zone (Sonic 3)
A water stage as early as the second zone? i'm sure many a child cursed to the heavens as they fell into the watery depths at the start of Hydrocity (and hopefully they didn't steer their fall into the spikes like I first did). But Hydrocity isn't what it appears to be at first, Hydrocity is about both the slow slog through water and the swift sprinting across its surface. It juxtaposes these styles to great effect, on top of this the underwater sections introduce the bubble shield eliminating air concerns as well as preventing certain turrets from damaging you. It's not maze like either, it's got some wide open areas to test Tails swimming ability and who could forget the pursuing wall of death to kick off act 2? Without a doubt it's one of my favourite zones in any Sonic game and it has great music to boot, I used to be an Act 1 man but i'm feeling the faster paced Act 2 theme these days.
Kind of a cheat for this thread seeing as it has no swimming mechanics to speak of for Sonic himself but here it is anyway.
Aquarium Park (Sonic Colours)
In an almost sacrilegious act Sonic can now essentially swim by cutting through water like a buzzsaw as well as tearing up any enemies he encounters. The approach to water here seems to be massive open tanks of the wet stuff mixed with land sections and while Sonic's saw like swimming is serviceable he needs greater mobility to keep it from being too slow which is where the drill comes in allowing Sonic to speed through the depths and take the various pipes scattered around. The water sections alone would be far too bare to make good stages so fortunately there's a good amount of land based sections, some stages have no water in at all in fact. While Aquarium Park isn't an outright amazing water stage it has the perfect blend of aspects that help elevate it, aside from Sonic's new approach to tackling water there's the stages unique visual style and it has what is in my opinion the best music in Colours.
Lava Lagoon (DKC2)
I've noticed that when a thread is made regarding good water stages I see DKC1 brought up a lot and while Aquatic Ambiance is a damn chill track I don't think it alone makes those stages good water stages, in fact they're pretty bare water stages all following the same style of corridor coral reef with evading (or swordfishin') the various sealife.
DKC2 brings in a ship hold for its main aquatic setting, one which is not only great in concept but lends itself well to the lowering and rising of water. Lava Lagoon takes an approach that ensures that this water stage is going to be anything but a slow and relaxing dip in the wet stuff, Lava Lagoon is going to make you swim a marathon or else you get boiled to bits. You jump on a seal, he cools the water for a brief period of time, you swim as fast as you can to either the next area of solid ground or to the next seal, rinse and repeat and by gum it works.
Sticking with 2D here but I also had Slimy Spring from Super Mario Galaxy 2 in my list.
I think this was from before Rayman Legends came out, admitteldy I don't know what stage I'd single out there as the best water stage off the top of my head, for Tropical Freeze it's easily Amiss Abyss.
I also tend to really like stages that have a good mix of land and water sections, going back to Tropical Freeze Panicky Paddles does this well.
