I'm not sure I can answer that question. I use different RPGs for different types of games, or when the mood strikes me.
Hmm... I don't believe D&D is a good roleplaying system, but the fact remains that I own a lot of sourcebooks for the new edition and I keep returning to it. Mostly because I know I'll always be able to get players for it. So maybe it's not strictly my favourite RPG, but you've got to respect a system that's become almost synonymous with the very term RPG and has become more or less universally known.
But yeah, I guess that still doesn't really answer the question...
I think the closest thing to a favourite system I have (as Rob Lang commented, "except my own"), on reflection, is The Window:
If you haven't already seen this game, you really should have. It's simple, light (very, very light) on the rules, and works for anything. This is a system where you can learn the basics in a single page.