Ebay or Amazon

For a small-scale seller, Ebay and Amazon present the easiest options for selling books to a wide audience: both are (relatively) user friendly, require no up-front payments, and provide sellers with some protection from fraud. 

So which one is better?

In truth, I use both sites because they offer a different style of sales.  Ebay--while offering some semi-permanent sales listings--is primarily an auction site where buyers bid on multi-day auctions.  Meanwhile, Amazon Marketplace offers sales via permanent postings with unchanging prices.

Ebay

Advantages: Especially since Ebay has begun offering 50 free posts a month it is the site with the lower fees.  If you don't sell, you don't have to pay.  Even if you do sell, the fees are relatively low: $0.50 for listings between $10 and $24.99 (full fee list here). Ebay also allows you to put up individualized images (helpful for really beautiful or unique books) and give in-depth descriptions.
Disadvantages: Ebay has two really big pains for sellers.  The first is that writing up a new listing--especially one for which they don't have a standard listing on file--is a long process.  You really need to carefully look up details on the book, take photos, etc.  However, the bigger pain by far is the fact that PayPal (a division of Ebay) holds seller payments for 21 days.  While there are exceptions and it is possible to have early releases if your buyers give you favorable reviews, it is annoying and, at times costly to have your money held by PayPal. 
When Do I Use It:  I typically have a few items up on Ebay at any given time and they are my more expensive, higher-profit books.

Amazon

Advantages:  On the Amazon Marketplace, sellers create listings and prices for their books which remain present until sold.  This means you can spend an afternoon listing a hundred books and then they basically sell themselves, unlike Ebay which requires more regular tending and updating.  I have almost my entire stock up on Amazon at any given time.  Also, when a book is sold on Amazon, payment is released as soon as you put in the tracking number.
Disadvantages:  Amazon is pricey.  While there are a number of variables, they inevitably charge several dollars--several times the fees on Ebay.  Make sure to price your books accordingly.  Also, you are required to buy tracking.
When Do I Use It:  I put almost all of my books up, especially the lower-end ones.

Final Analysis

Neither one of these services is perfect, though if you have the patience to update Ebay and wait for payments to be released, it is almost always the more profitable option.