Ebay will get you the best deal most of the time. Brand new games can sometimes be 5-10$ off the retail price, but you don't save much after shipping. I wouldn't reccomend going to random webstores, as many of those are scams.
The vast majority of my PS3 games purchased online came from Amazon. They're usually discounted a bit to start, free shipping, etc. Do your best to watch for Gold Box deals on PS3 games, they've been fairly common lately.