Beyond The Lamb and Abacab (coincidentally my two favourite albums of theirs) I'm not that fussed about any of the covers. I liked that Abacab originally came in different shades. Trespass is pretty good, especially with the knife slash. As mentioned above, I too like Three for its colour palette.
I don't mind the basic idea of the shapes one but for me it's ruined by the awful type face and the use of the shapes in the track listing on the rear cover. I think it'd be actually a good cover without the name on the front, just the image, then on the back 'Genesis' not in that appalling font and the tracks listed without the whackily tilted shapes next to them. But I get why it's so widely disliked.
IT, WCD and CAS are all poor. Of the live albums 3SL is by far the best - stark, simple with the single image that captures the excitement of a Genesis show better than any of the imagery on any of their other live albums. Live is good, SO the worst with its clinical front cover and lumpen formulaic inner 'collage' so beloved of rock bands' live albums back then.