Jeff Bezos was a solo founder when he started Amazon in 1994. Employee #1 (Shel Kaphan) was brought on before incorporation, but says Jeff was the founder (http://www.geekwire.com/2011/meet-shel-kaphan-amazoncom-empl...)
Andrew Mason was a solo founder of Groupon, started with $1 million seed money from a former employer.
Lots of people like to point out Drew Houston of Dropbox as another single-founder success story (and it is!), but he did have a co-founder by the time they presented at Demo Day (if not before YC started, I can't remember which).
However, he did apply as a single-founder. Here is his YC S07 application: http://dl.dropbox.com/u/27532820/app.html
The single founder was Philip Kaplan (although he's not you're average single founder).