I think up a lot of theories (because yeah, I have no life), so I'm going to dedicate an entire thread to me. I change topics a lot, but feel free to go back to an old one to talk about it if one is missed.
First up: Termina.
Some people say that Termina is just another world that Link goes to in his adventures, and others still say that it's a parallel dimension of Hyrule. I think that the actuality of Termina is revealed in the instruction booklet for MM.
It says that Link went on a journey of self-discovery, or something to that extent. This makes me think that, rather than an actual land that Link goes to, Termina is a state of mind. It's a world that exists solely in Link's mind, where he goes on a quest not to save Hyrule, but himself. It makes sense, MM being the only game where Ganon doesn't (even indirectly) influence the flow of the game. The Clock Tower represents Link's fragile childhood, about to be crushed under the 'fake moon' that is the reality of it all, of being forced to save the world and sacrifice himself countless times in the process.
The beings that he transforms into are other aspects of the whole. the Deku Scrub is the small, nature-loving creature. It puts on a tough facade, but is actually rather weak. The Goron, although just as easily hurt, can be untouchable when it puts up it's 'wall', and relies on brute force to get past obstacles. I haven't thought of something for the Zora yet.
Well, that's my theory so far, and I'm sticking to it.
What do you think?