The two that really stand out for me are both DC products: Matt Wagner and Guy Davis' Sandman Mystery Theatre and James Robinson's Starman.
Honestly, I didn't much care for most of what Marvel was doing in the '90s, and stopped reading most of their titles then (permanently, as it works out, though that wasn't my intention at the time), so I can't really speak to how they hold up.

Ah, the meek. Playing the long game.
Sneaky bastards.

--Denise Mina, Field of Blood