Anything you have manually added in or changed in the GarrysMod/garrysmod folder, such as any custom configs, any files You've manually added to Addons Folder, maybe your screenshot Folder?.This is where any custom things you do in-game on a server will be saved (Dupes, Wire Mod E2, Chat Box Customizations, and So on) By Gmod. Probably the most essential folders to back up is your data folder.

(I will opine my opinions at the end if anyone is interested in Why I think these things Happen. So I decided to post here on 'how to do a full clean install of Gmod' because I often run into posts about Issues that often can arise and be contributed to how Badly The game and Steam manage add-ons and Data.