My favourite Allen films are "Annie Hall", "Manhattan", "Hannah and Her Sisters", "Everybody Says I Love You" and "Crimes and Misdemeanors".. thats a tough top 5.. since he made other great ones too.
He really shows signs of slowing down though, yeah. He once said though that if his movies aren't making a profit, he's doing something right. I disagree now because I think his films seem to be aiming at dumber, simpler audiences now, and thats what making them not that good. I'm sort of surprised by this though.. since Bergman was his main influence/inspiration and he made great films up until the day he died, whereas Allen can't really think of something great anymore.