@ Supertoad
I don't think I've ever tried that map glitch I keep hearing about. I normally don't use glitches to cheat in games anyway.
Most of the time those things cause games to lock up and the possible loss of your save file.

Use it in a side-view room in a dungeon, and if you don't get stuck in the wall (what happens is the glitch causes the next room to load, but keeps Link on the same screen position), you'll return to the top-view rooms and you'll be able to swim everywhere, including through walls. You'll eventually be able to move between dungeons and through caves.
I've used it before, and I'm pretty sure this won't glitch up your save file. At least it's never happened to me.

There's a glitch in the original Metroid that lets you pass through floors.
You can get the varia suit way early. Everytime I try it the game freezes up though.