Mod Organizer will alert you to any mod conflicts and allow you to resolve them easily.Mods that have not been properly put together by the author can be cleanly installed to improve game stability.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. Profiles can be created which allows you to have multiple configuration files so that you can experiment with settings safe in the knowledge that you have another profile with the default settings to fall back on.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.