As much as I love Babylon 5 and Sense8 (and his own comic series, Rising Stars), everything I've heard about his Spider-Man run has sounded awful. The one exception is the 9/11 issue which I have read.
I quite liked most of JMS's run on
Amazing Spider-Man. He did some terrific things, like having Peter become a teacher, having Mary Jane begin a theatrical career, and best of all, having Aunt May discover that Peter was Spider-Man, rethinking her whole perspective, and becoming his confidante and avid supporter. My 2008 novel
Spider-Man: Drowned in Thunder was set during the JMS run (as well as Paul Jenkins's contemporary run on
Spectacular), and I really liked making use of the elements he introduced, especially Peter's relationships with MJ and May and his teaching. By coincidence, Jim Butcher's
The Darkest Hours, Keith DeCandido's
Down These Mean Streets, and my novel are all set at roughly the same point in JMS's run, the brief window between MJ starting her theatrical career and Spidey joining the Avengers. So the omnibus edition collecting all three novels (as
Marvel Classic Novels -- Spider-Man: The Darkest Hours Omnibus) works nicely, as they're nearly consecutive stories.
There were things about JMS's run I wasn't as fond of, though, like the whole Morlun/spider totem business, though that was only an occasional recurring thread. And I hated the ending with
Back in Black and the whole Mephisto business, but IIRC, that was at editor Joe Quesada's insistence and JMS just tried to make the best of it. Also, JMS's handling of Tony Stark in the
Civil War storyline was probably better and more nuanced than anyone else's.