We just got our servers set up with SVN which works great. Wordpress upgrades and plugin installations are managed manually, which all goes through SVN as well, but I can't work out a good way to version control upload directories.
The best solution I can think of is to periodically go into the folders, look through the images to make sure they are legitimate (no self-unpacking shell scripts, etc) and commit them... either that or svn:ignore the entire folder.
Is there a better way to do this? All the discussion I can find on Google has to do with using SVN for Wordpress installs, not dynamically managed assets.