I think the best Yes album is Close to the Edge, but my favourite track is Roundabout which is on Fragile.
Can you think of any artists/bands where your favourite track is not on the best album?
Far too numerous to mention...dozens, if not scores, or even hundreds, in fact this sort of thing would literally drive me insane trying to think of examples, but here's just a few -
Fave Van Morrison song - Into the Mystic .... fave Van album - Astral Week
Springsteen - track, Jungleland...album - Darkness on the Edge of Town
Dylan - track, Ballad of Hollis Brown....album - Blood on the Tracks
Zeppelin - track, When the Levee Breaks....album, Physical Graffiti
Stones - track, It's Only Rock n Roll...album, Exile on Main Street
Genesis - track, Ripples....album, Then There Were Three