This happened to me in early summer of 2007. I was actually at the airport to join another program when I followed my gut and took a chance with my Y Combinator application instead. I was subsequently interviewed and accepted, so it worked quite well for me. I would, however, encourage everyone to weigh their options before following their guts as in the end you may get no offers by taking a risk like I did.

Probably part of what prompted my decision was how much integrity this other program didn't have relative to Y Combinator (offering perks and having integrity are sometimes inversely proportional).