Well, I've never been to a Genesis concert, but I know a lot of recordings. I have to say the Three Sides Lives Encore Tour is my favourite. Perfect balance of old and new stuff, and they were on fire during that time (1981-1982). Interesting arrangements (DOAV > BTL, LLDOB > WOTS...) too.
And that Marquee show... Wish I was there !
Another is the Abacab Tour. Not my favourite album, but the musicianship during the live performances is unbelievable.
One last could be the Trick Tour because of its special sound - thank you Bill Bruford ! They didn't always match with him, sometimes it sounds almost off (listen to the video of Apocalypse, Bill tries to play some weird 16th note triplets...). But I like when things go a little bit out of hand, especially with bands that are not known for that.
Otherwise I like tours with some hidden gems (Mirrors Tour with Fountain of Salmacis, Duke Tour with Back in NYC...).