It's not "Imagine". That seems to be the popular answer to this question and it bothers me. I may be in the minority with this one, but I like "Revolution No. 9" and "The Ballad of John and Yoko", and my second favorite John song is "Instant Karma", but mostly because it is all wacky.
My favorite? "Watching the Wheels". I've felt that way before, everyone says one thing and offers advice about your situation, but you've got it under control, you know what's up. Along those lines, "Cold Turkey" is a pretty good one. :)
Mr. Lennon, your music will live on forever as long as we remember it and as long as Yoko keeps "finding" recordings in the linen closet. :)
RIP John and, you know, Happy Birthday