I want to have a bootable flash drive that's fully encrypted. I have not tested, but seem to like, TrueCrypt, which provides a fully encrypted system and has lots of other features I like (for instance, hidden volumes). Unfortunately, it seems, system encryption is only supported for Windows, although I'm not sure why.

The crux here, I guess, is that you need a boot loader that is capable of asking for your password and decrypt the disk, at least the part that contains kernel and initrd.

An alternative might be to have an unencrypted boot partition containing a more powerful system which will decrypt and mount the main partition. However, this brings up the question of whether you're introducing data leaks. Depending on the specific scenario, I may lack the experience to assess if this is a problem. So I'd strongly prefer a fully encrypted disk or a similarly straightforward alternative.