In another answer I wrote about uninstall/activate/deactivate/upgrade routines. I guess most of the comments already tell it, but to sum it up:
- Uninstall: Remove everything, your plugin added
- Deactivate: Do nothing
- Activate: Do what your plugin needs.
On Uninstall the user simply wants to get rid of the plugin, so it’s fair to not leave any mess. Remove everything including tables, etc. Ok, if you got tables, you should maybe tell the user what your plugin is going to do. A simple alert() should do the trick.