International rights, for one. Publishers would be happy to hang onto them, and if you don't have an agent you might as well let them, because it's VERY hard to sell foreign rights without an agent. But that's something they'll let go if you ask. Other ancillary rights, as well--audio, book club, film, TV, videogame, toy, etc.. They're not really in those businesses, and if you have a better way to shop those rights, you can keep them without much of a fight. They'll give on the subject of how many author's copies they'll provide--always ask for more than they're offering. There's a standard clause saying that if they ask you for changes and you don't make them to their satisfaction, they can pay someone else to make the changes--that'll go if you ask. Anything about the delivery schedule is open to negotiation.
They'll even budge on money, sometimes. That's a harder fight, though--they know what their budget is, and while they might try to low-ball you, the fact is that they have already committed those dollars to you and other dollars to someone else. My agent has often been able to nudge them up more than enough to cover his percentage though.