Paypal's 2.9% plus 30 cents, I think.
You can't really count the Paypal fees in the same boat. If you were WalMart, you would pay Visa and Mastercard a percentage of every sale paid for with a Visa or MC. Part of the Paypal fee goes to MC and Visa and allows you to take those cards (assuming you're Premier or Business). This would cost the average non-business seller a whole lot more if they had to set it up directly with Visa and MC. (I think Visa/MC charge a flat fee per month, plus a percentage of each transaction.)
Amazon does tell you what the fees are before you finalize the listing, but damn, their fees are high.
I sold a DVD set recently for 64.99, with a 2.99 shipping credit, and the Amazon fees totalled 11.54. The 2.99 actually did cover shipping (yay media mail), so that was good, but still.
Ebay and Amazon provide a marketplace for millions of people to buy. In addition to that, they offer 'secure' methods of payment for both sides (let's not get into the alleged abuses by Paypal and Amazon Payments). They're also two of the biggest names on the net. Those factors are worth something. Yes, you could do Craigslist for free, and be lowballed or ignored, and that's if not you're not asked to send the overpayment to Nigeria.
Trading sites are a great option, but even there you have to be careful (I have traded games before where I've lost money on the transaction due to shipping, and since you pay shipping, some cheaper things aren't worth trading, whereas I have sold things on Ebay that were virtually free, but the buyer paid postage and covered my Ebay fees).
I do prefer selling on Amazon, however (at least for noncollectible goods). I like not paying until/unless it sells, and I've found that people are often willing to pay more on Amazon than Ebay for the same item, I'm not sure why.