Well, your cheapest bet is always eBay. As long as you're patient, and know when to seize a nicely underpriced Buy It Now, you'll make out much cheaper than buying from an on-line store (usually at least 50% cheaper). The problem with eBay is that each Seller has his own opinion of what "Mint" vs "Good" is, and there's always the chance of being shafted by a dishonest shmuck.
I've done a fair bit of business with on-line stores. The three stores already mentioned (Noble Knight, Hit Pointe, and Dragontrove) are all legit, and I've never had problems dealing with them. Of these, Noble Knight's probably got the most expansive stock on-hand, but their website can be a pain, and the checkout cart can be a little wonky.
I just now tried a new seller: The Hero Factory (
www.theherofactory.com). As I only bought the stuff last week Thursday, I don't know how good he grades his stuff or whether or not I will actually receive the items. But his response time to e-mails is quick (so far never more than 24 hours), and he kept me informed every step of the way up to shipping. And on average, his prices seem cheaper than other places, though not as cheap as eBay.