Nine-tenths of the advice out there urges writers to obtain an agent before negotiating your book contract with a publisher. Here is an excellent blog (written by editor Moonrat) explaining why having an agent is essential.
That being said, sometimes it's easier to find a publisher than an agent (okay, neither one is easy, but I've got a publisher and no agent.) I found it tough to locate information about publishing contracts online, and the library and bookstore were also little help.
The very best information was on two different agent blogs: the "Agenting 101" series (look for it on the right hand side of the page. There are eleven references) on the Pub Rants blog by agent Kristen, and a blog entry called "Ten Things to Know if You Go Commando" on agent Janet Reid's blog.
Another site I found helpful showed a sample author contract, just to give you an idea the document may look like: www.writecontent.com.
Negotiating your own contract still isn't the way you want to go if you have a choice. But these articles (the "Agenting 101" series is really almost a class in publishing contracts) can go a long way in helping you out.