I'm trying out Unison File Synchronizer as a way to keep my two machines at work in sync. Unison inherits many concepts from source code management tools like CVS and SVN, and can manage bidirectional updates (even merges). I've done a test sync, firing the contents of my Powerbook over on top of my deskop's home directory. It took only about 20 minutes or so to copy stuff over, but a long, tedious process of approving or reconciling conflicts made the process last many times longer than that.
It would be cool if Unison could have a flag that said "hey, if there's a conflict, trust the Powerbook, and blow away the desktop" or vice versa. So I didn't have to hit "." for each of 20,000 files...
There are precompiled binaries for MacOSX, including both a GUI and command-line app. I had zero luck with the GUI version, but the command-line app was trivial to use.
If this works out, it will replace the last function that I rely on my now doomed .Mac account for...
Update: Between having multiple sync profiles, and being able to set the -auto and/or -batch flags, this could be a very usable solution! I've tried disabling .Mac sync for a while to see if I miss it.