This is a good list, but I think we need to include the underwater levels in Metriod Prime and Prime 2. (Maybe they'll do another list with newer-gen titles.)
As for this list, it's a toss-up between Mario 64, Zelda, and Star Fox.
Now, Mario 64 is annoying, but never really a dealbreaker. The eel thing scared me as a kid (I WAS 8) but overall, it was quick and painless.
Zelda's level was in fact, a pain in the ass. You had to change the water levels, the dungeon is non-linear after every other dungeon being the opposite. I finally get to the door where dark link is, and can't get through because I FORGOT A FREAKIN SMALL KEY. But overall, I overcame the obstacles and beat the boss. It was hard, but never impossible.
What is impossible? STAR FOX 64's UNDERWATER LEVEL. First off, we've had levels with the landmaster. It's a weird perspective, but manageable. The underwater level? Every enemy somehow does about 2x damage than regular, maneuvering with close to ZERO visibility is impossible (I mean space is pretty dark... It takes some kind of a mastermind to make WATER darker than SPACE.) if you didn't have infinite torpedoes it would be beyond impossible, except that every other enemy does that annoying blast thing that does massive damage over a certain area, and unless you memorized the strategy guide or gamefaqs guide for this thing, the boss fight is INSANE. What kind of clairvoyance do I need to beat this guy? I hate, hate, hate, HATE this level.