When you pre-order in a store, you pay them 5-10$ and that means when they get their shipment of games in, they'll keep your copy in the store until you come and get it--they won't sell or "run out" unless they get omre pre-orders than their shipment.
When you pre-order online, I don't believe they charge your credit card until the game SHIPS, but when you pre-order online, many times they'll send you something special--like a CD with promotional info, or like Frsblch said, a spot in an online beta.
Personally, I wouldn't bother pre-ordering unless:
1) I KNOW the game will be fantastic.
2) You get something really useful/cool by doing it.