This did not deter us from continuing; our company was profitable already, and we worked our butts off for the next few years (without any reasonable perspective of ever getting acquired, or even growing the company to be big). The work was interesting, and for a company that size, we had a surprisingly large impact (indirectly) on the wider world, but it was heavy toil with little reward.
Either way - history then shifted under our feet, and it turned out in 2010/2011 that we had the combination of technology and team that out of a sudden had become pretty important to Google, and then after a long and painful negotiation process, we got acquired in 2011. Not a gangbusters acquisition by any stretch of the imagination, but one that worked out nicely for everyone involved.
So perhaps the takeaway from this is: YC is great, but perhaps the great redeeming quality of modern capitalism is that you do not require gatekeepers in order to be successful. "You play shit that they like, and people will come, simple as that." - e.g. if you build a product that people like, people will give you money to build more of that product. Decentralized decision-making and the ability to bootstrap with nothing but a compelling product may be the one thing that led to our current economic system to out-compete the others.
When we started the company, I wanted to build X. This was a huge endeavor, and I knew that on the way to X I'd need to build Y and Z; so I ended up building Z first, then used income from Z to bootstrap development on Y, then I got sidetracked a bit on B because we found a surprising application of our technology to a different field, and just when I was about to get back to X, we got acquired principally for B and Z. So up until today, we have made very little progress on X itself, but that doesn't matter :-)
So if you're rejected from YC, don't despair. Use it to re-examine what you're doing, understand that investment is like dating (some people are just not made for each other, and it will end in horror if you pretend to be someone you are not), and then channel your disappointment into velocity :-P
(PS: pg, if you folks have any notes whatsoever on reasons for rejection in the first YC batch, I would love to have more background info - but it is also pretty understandable if no memory at all exists ;)