Custom Content (CC) is objects, clothing, hair, etc you can download from 3rd-party sites to your game. Those are not endorsed by EA. CC is made with tools that were created by the community and not made with official tools. Custom Content can make your game a whole lot more fun but it’s dangerous as well. Every patch that EA releases can bork your CC. There is also CC that was always bad to begin with. It can crash your game, cause your lots to become blue holes or make your Sims look like monsters. Some of it is listed in the section Bad CC of this blog. More info can be found over at the MTS SimsWiki
The EA Store
EA offers many objects and clothing through their Store. Items in the Store can be bought with SimPoints (which can be bought for real cash at their site). To me, it’s a little unclear if Store-Stuff counts as CC or not. If you use the option to deactivate all CC, Store items are removed as well.
For the patching process it’s not necessary to remove those items (in most cases anyways) and as long as you don’t install them any other way than through the launcher, those items should not get borked by a patch. Despite all this, there are a lot of items in the Store that are faulty though. A rather incomplete list can be found here: List of Faulty EA Items