Rolling Stone updated their top 500 songs list, which they made in 2004, to take a new broader look at pop and include more recent influential pieces. I scrolled through pretty quickly and only found one track by any Genesis-related artists:
Article here: In the Air Tonight is at 219
I was kind of hoping to see something like Land of Confusion or No Son of Mine make the cut, or M&tMs Silent Running, Miracle, or Living Years, or even Sledgehammer or In Your Eyes from Gabriel, but I didn't see them (perhaps I scrolled by too quickly)