Some of these runs started in the 80s or ended in the 00s...but I'm specifically referring to the 90s runs.

Still stand up:

Marvel:
Quasar
Avengers (Busiek/Perez)
Untold Tales of Spider-Man
Thunderbolts
She-Hulk (Byrne issues)
Excalibur
Guardians of the Galaxy
X-Force/X-Statix

DC:
L.E.G.I.O.N. & R.E.B.E.L.S
Suicide Squad
Young Justice

Titles from the 90s that do not stand up:

Marvel:
Fantastic Four (Heroes Reborn issues and Claremont issues. Ugh!)
Fantastic Force
Iron Man
Force Works
Spider-Man: All titles from the Clone Saga on through the Byrne reboots and beyond...
Silver Surfer (Ron Marz-written issues)

DC:
Teen Titans (hideous reboot) + Team Titans
Superman (after the whole Death of Superman saga and onward)
Justice League titles (very tiresome for some years before Morrison reboot. Worst was J)
Wonder Woman (Byrne issues)

All Valiant titles after the Shooter era
Continuity Comics (Adams' work seemed very dated even then. Would have been popular 20 years earlier)
Ultraverse titles
Pretty much the entirety of Image comics, except for McFarlane's Spawn which was exceptional. Everything else...aye yie yie...!