The obvious answer is "advertising" but I've heard of a lot of decently popular sites that don't make much on advertising. How else do you make money? are they just hoping to get bought out?
And for those who do have a "premium" service, how many customers actually pay for it?
EDIT Thank you guys for you answers. I'd like to emphasize the second part of this question, how hard is it to get users to sign up for the paid version of a website when you have a free one? An example I'm thinking of is Tripit. I use it, but I use the free version, and I don't really see a reason to sign up for the paid one... On the other hand, I use freshbooks, and did pay, because I needed more than 3 accounts.