Which one will pay you more? (don't factor in stock options. Odds are they will be worth $0).
I play them off eachother for a higher salary (or other perks... e.g. more vacation time, signing bonus, etc).
The hiring process is long and expensive because excellent candidates are very very difficult to come by. Startups don't like to waste time hiring... they want to spend time engineering. If you're excellent then you've got all the negotiating power on your side -- UNTIL you sign. Even if you only had one offer, you should still try to negotiate for a better contract.