It's not a comic, but Spider-Man: The Darkest Hours is a pretty great novel that feels like it could slot seamlessly into the comics that came out at that time (this being circa the early JMS run). It also addresses some things that would be followed up on in the comics in one way or another (namely, the whole totem thing and Morlun having a family) and does them better. Also it has maybe the best use of Rhino outside of Flowers for Rhino or that Gauntlet story.