drivel has a lot of good points. I'll add a few from my own experience.
Realistically, probably better to hold the line at a no salary difference (or very small) and make sure that the benefits (401k, healthcare) are at least available, though they will certainly not match a bigger company. So benefits are your "give".
I agree about the 2-3% of outstanding shares idea, however your chances of getting stock that cannot be diluted are zero. Dilution will happen to the point that an initial 3% will be .003% by the time the stock has any value. It is the nature of vulture capital.
You will work a lot more hours. However, your contribution will be much more substantial to the product/value of the company. You will get your hands in a lot of varied work and learn in one year what would take you 3-5 years to learn in a big company where you will likely be pigeon holed.
You will likely never be directly compensated for those extra hours, but again you will have much more experience. Therefore you will get more job offers in the future and your next job will pay more. That experience will help you choose better situations for yourself in the future.
If you go for the big company, be prepared for mind numbing meetings, procedures that stifle any actual work getting done, and being the guy who does just one little thing in a very large machine with little impact or visibility into the rest of the machine. You will have a decent salary and benefits, but no more job stability since the company will do mass layoffs every time they lose a contract. You could eventually move up to middle manager. This is the person that upper management puts in between them and workers. Their primary purpose is to listen to worker complaints and have absolutely no power to do anything about them. And they get fired if they escalate those complaints to upper management.
My experience is very positive with small companies and start ups. Large personal contribution and personal satisfaction. Stock options paid off once, but in a very small way (calculation of hours above 40 for 3 years, I made about $4/hr, about enough to buy an economy car). Now I make a lot more due to experience and can hit the ground running anywhere on any type of project, therefore make more money. Not so bad. Mostly, I still work at small companies.
Bottom line, if it sounds interesting and you are willing to take bad with the good, do it.