A while ago I got the craziest idea that I'd document Ocarina's save file format for the purpose of finding glitches, in an attempt to both make one hell of a save editor and to uncover some hidden bugs like the mystery behind why the ice around King Zora would mysteriously disappear (turns out it had nothing to do with the game setting the wrong flag, King Zora is just a rather impatient fellow and if he loads before the ice does he melts it on his own).
Well today I've just completed mapping out the permanent scene flags for the 8 major dungeons, minus the flags used to light up which rooms have been entered (because I just don't give a damn about them). You can find the tables at ZeldaSpeedRuns because I can't figure out how to upload attachments and it's really late right now.
There are also other odd things listed like various actor flags and cutscene flags, and things that are never saved like Temp Switches.
One rather interesting thing I discovered was that Nintendo was pretty careless with their blue switches. Most blue switches set either a permanent flag, or a "dungeon" (cleared only when using certain exits) temp flag, rather than using a "room local" temp flag. The consequence of this is that dying on a blue switch causes it to stay set until the room is left, resulting in a few puzzles becoming complete
http://forums.zeldaspeedruns.com/index.php?topic=374.msg18660#msg18660
