Hi,
Did you just disable the plugin or did you completely remove it? Also your htaccess file and wp-config may temporarily need to be writable to get htaccess and such back to before the install. Does W3 still have entries in your htaccess file? Delete them (the cache changes) if you still do not want W3 total cache. You can also reinstall W3 and then uninstall (as long as htaccess and wp-config writable - don't forget to change back when you are done) to clean up the files it changed.
Hope That Helps