Hey Jude for me, hands down. It's probably my favourite song, ever. It's great lyrically, melodically, the recorded version is amazing [The orchestra totally adds to it -- at about 3:40, 3:50 where the louder part comes in ... man. Musical orgasm if ever there was one.] the unity of the song . . . I mean, WHO else could write a song that goes "na na na" for around FIVE MINUTES like that and it'd still be beautiful and enjoyable? Paul. Friggin'. McCartney. <3 Much love.
Let It Be is, IMO, an incredibly close second. But it couldn't surpass Hey Jude. Yesterday is a great song, but... I dunno. It can't even touch Hey Jude, man.