In my opinion, Marvel gets too much-undeserved flack and bad rep due to some really bad stuff that did come out, but other really good stuff did as well.
I wanted to list my favorites from the era, encourage others to do the same and hopefully turn some hearts and minds:
(In no particular order)
Marvels by Busiek and Ross
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Nicieza's run on adjectiveless X-Men - best X book of the 90s for me
Ellis' run on Doom 2099 - the beginnings of a great writer
David's run on Hulk - a classic, everyone can agree on this one I think.
Harras' (sans Kavanaugh) run on Avengers - may be an unpopular opinion but I really enjoyed the Gatherers Saga. Shame it went so badly off the rails afterwards.
(latter half of) Gruenwald's run on Captain America - another classic run.
(early) Jurgens' run on Thor - despite the writer's name here it was a return to form for Thor's solo book and lasted over 80 issues.
Busiek's run on Thunderbolts - the best new concept of the 90s.
Busiek's run on Avengers - best revitalization of a then very badly damaged franchise.
Loeb's Cable - made Nathan a must read.
Claremont's Fantastic Four - brought the book back to form after years of mediocrity.
Kevin Smith followed by David Mack Daredevil.
Busiek's run on Iron man
Krueger and Ross Earth X
Age of Apocalypse
Fatal Attractions
I'm likely forgetting something, I'll edit the post as needed.
Thanks for reading.