I don't think the use of affiliate sites like Ebates or Fatwallet affects price, though you are right that Priceline could probably do this if they wanted to, I had never really considered the possibility myself.

I've never tried Moe Money Maker, but you're also right there, it would have to affect performance, and while I heartily recommend Ebates, I avoid tools like that from any site. Whenever I'm shopping online I go to Andrew Crams RewardsDB.com to compare different offers in terms of cash back versus mileage, sometimes the miles are more attractive. (I'd give you a direct link to the page you need to go to, but that site keeps evolving and it can be difficult to navigage, go to "Shopping Rewards" in the top menu, then to "Online Shopping", then to "US & Canada" and select the first letter of the merchant you are checking.