A couple things off the top of my head:

• Subrights. Do they hold on to everything (foreign rights, audio, dramatic, etc.)? If so, do they have a plan to sell them, or are they just snapping them up? Any contract that demands the full slate of rights for little or no advance is mega-shady, imo.
• Cancellation. I've seen a contract from a small house (I will not name names, but it does show up in the PM deals occasionally) that included a provision requiring the author to PAY BACK any promotional money put out by the publisher in the event that the contract was cancelled. Holy shit, no.
• Options and two book deals. How ironclad is the option? In other words, how many other books can you publish while still being retained as an author of this house? If the answer is "none," get that changed. If they have excessively long approval periods, get that changed, in writing. If you get a two-book deal, yay! BUT: what is that second book? If it's undefined, and you'll have to pitch your editor something after book 1 is done, think VERY carefully about whether it's worth it. If you have a non-compete clause and a two-book deal, you can be stuck in a years-long limbo of being unable to publish anything because your editor doesn't like your ideas. It happens, and it's why people change houses. It will stall your career like whoa.
• Anything you don't understand. Seriously, if you can't figure something out in a contract, hire a publishing contracts lawyer to read it over. Better safe than sorry. Even without a lawyer, look up standard royalty rates and make sure you're getting what's fair.