Kris Rusch has a really scary post on the contract (actually a Terms of Use agreement, wow) that you have to agree to with a certain e-publisher.
We can quibble about whether or not a particular royalty is a good deal, but honestly, I feel like the primary advantage of self-publishing is simple: You don't give up ownership of your work. That is something that sounds very simple but that puts you in a far greater position of power.