I suppose The Waiting Room is the obvious choice, the only example in their career of a free-form jam. In a way, it's their Revolution 9. I love the second half, it's one of my favourite pieces of Genesis music. I always liked the rare occasions when they got a bit dirtier and edgy. If part 2 of TWR is at the end of the Genesis spectrum I most like, the opposite end has the stuff I really dislike - the shiny, twee, fluffy stuff like RA&B, Mouse's, Snowbound, Scenes.
Who Dunnit, while not a favourite of mine (although I don't mind it), was kind of a clever move by them. Abacab is generally a very conscious step away from their (and the fans') "safe" zone, and that track sums up that move. I did read Banks saying they knew it would annoy the hell out of lots of fans, which is why they did it. I like that approach.
In some ways I think Happy The Man is an unusual one in that it doesn't feature much (or any?) keyboard and lacks those trademark chords. Harlequin is similar.
More Fool Me does stand out, being a quite soulful and melancholy guitar-and-vocal duo, something they only did that once, I think. I like it a lot and it shows how varied their work is. Side 1 of SEBTP remains for me probably their finest bit of track sequencing in any album.
Oh and of course, Horizons is pretty unusual.