So after switching to BittorrencSync for a few months (which was working well) they bloated out the software and made it no longer completely free. Next I tried Synching, but it had issues with files that were open while it was syncing (for example KeePass).
So now its back to dropbox with EncFs encryption. DropBox’s synchronization just works really well. They have fast servers, and over all its a great solution. Only issue is trusting them, but so long as we are encrypting everything that doesn’t matter.
Additionally what i’ve done is created a small script to run on any freshly formatted computer i’m trying to setup for use.
This makes my dock sync across all computers, the screen shot default location to dropbox, and documents being stored on dropbox.
mv ~/Library/Preferences/com.apple.dock.plist ~/Library/Preferences/com.apple.d$
ln -s ~/Dropbox/File/osx/com.apple.dock.plist ~/Library/Preferences/com.apple.d$
defaults write com.apple.screencapture location ~/Dropbox/Screenshots
mv ~/Documents ~/Documents.old
ln -s ~/Dropbox/Documents ~/Documents