From the YC FAQ (http://ycombinator.com/faq.html):

We've already been working on our startup for a while. Is Y Combinator appropriate for us?

We've funded a lot of startups like that. In fact, we especially like them. We can probably help any startup that hasn't already raised a series A round from VCs.

Don't incorporate, though, if you can avoid it. It's easier to start with our paperwork than to transfer an existing LLC or S-Corp to a C-Corp.

We've already taken some funding. Can we still apply?

Sure. We've funded many startups that have.