Mod Organizer can show which mods are being used with which saved game.Saved games can be cleaned if mods are removed (otherwise saved games can become unstable or fail to load altogether).Mod Organizer can fully integrate with Nexus Mod Manager so your mods downloaded using it can easily be moved to Mod Organizer.Mod Organizer can also filter saved games based on profile.
You can also have different mods running in different profiles. Rather than being installed all together in the game folder, instead they are installed in their own folders to allow mods to be un-installed quickly and cleanly.
