Kerbal Space Program

Custom user-defined subassembly categories are stored in a config file in GameData/Squad - which means they're global across all saves, even though the subassemblies themselves are not. So you put a subassembly in a category in one save and if a different subassembly in another save happens to have the same name, it moves to that category too. Also, if you upgrade the game by backing up saves and overwriting everything else, the categories are lost.