Apparently I haven't written about this before, or at least I can't find the post, so here goes. I have a custom file sync program I wrote myself, called MediaSync, in order to synchronise collections of files across very disconnected computers that don't have any way to connect with each other except flash drives. I wrote it for picture and video files, but it works on any files, of course. Since Windows Live Mesh shut down, our office network blocked BTSync and my personal photos and videos collections are too big to fit into Dropbox, I have opened up development on this project again, and it's going great.
Basically, it takes an index listing of every machine that participates, checks which files need to be copied around and puts them onto a flash drive. The unique feature it has is space limitations - you allocate, say, 2GB on your 8GB drive, and the sync copies will only ever take up that much space. It might take a few trips to get fully in sync, but you can run it on whatever flash drive you have lying around.
If you can, the whole process would be better served by a large external hard drive and SyncToy, but it's kind of neat to watch the collections gradually get in sync over the course of a week.
The big disadvantage is that it won't update or move files yet. If you rename a file in one location, MediaSync will detect that as a new file and will copy duplicates back and forth between machines. I'm working on that feature, to propagate renames instead of duplicating files, but it could be a while.
Mokalus of Borg
PS - It's not ready for the general public yet, though.
PPS - It still runs in a text-only interface and requires editing XML for full functionality.