That's interesting... our school has spirit week (run away!!!), but we've never had an opposite gender day. It would be fun, but awkward in our situation for the reason you pointed out; what are we supposed to do? The purpose of the event is to dress the opposite of your gender, which would be referring to your physical sex, which means you would go in boy's clothes, but since we're all actually male (and probably amazingly proud of it for such a crappy status), we would wear female clothes. Unless everyone who saw you knew you were trans (wearing girl's clothes), they'd hold it against you or assume you forgot. Since nobody knows, doing something over-the-top female would make it obvious you did it on purpose for that day, but then you can expect lots of weird remarks and questions.
It all boils down to one question; do you feel comfortable with it? If you think your school is open enough about those kinds of things, and you don't mind people knowing, go for it! If you don't want people to know, and they ask, just say since you normally wear boy's clothes, you thought it would be more in the spirit of things to wear something totally opposite to your normal clothes instead of what you'd normally wear. (I hope that made sense

) It's a believable excuse.
The annoying thing about that for a spirit day, is that, if you wear your normal guys clothes, people will look at you as female that day. If you wear girl's clothes, people know you as female (tomboyish), so they'll be confused and will ask tons of questions. It's a lose-lose situation. But I like Alexmakenoise's idea!

But whatever you decide, good luck!