What stuff are you talking about? Apps you bought in the app store? If you UPDATE you'll be fine. If you restore you'll lose it.
apple keeps a record of all of your "purchases" which includes free apps... this is so that if the price goes from free to $0.99 in the future, you have already purchased it (for free) and don't have to spend the $0.99 to get it again
i was talking about my jailbroke stuff, bought a few apps on cydia
sakurik keeps a record of your purchases also (only actual purchases)