Let's see, there's a lot from that era that I watched and liked, but my most favorite ones would be Slayers, Tenchi Muyo, Ranma 1/2 (excited for the remake), Sailor Moon, Nadia: the Secret of Blue Water, Dirty Pair Flash, Burn Up Warrior, Mikan Enikki, Bastard, Video Girl Ai, Pokemon, Dragon Ball Z, all Ghibli movies, Otaku no Video, Sally the Witch, Dr. Slump, Fushigi Yuugi, Ruin Explorers, Gunsmith Cats, Cat Girl Nuku Nuku, Captain Tsubasa, Martian Successor Nadesico, Saber Marionette series, Those Who Hunt Elves, Plastic Little OVA, Vampire Princess Miyu, IRIA: Zeiram the Animation, Orphen, Magic Knight RayEarth, Armitage III, Magic Users Club, Revolutionary Girl Utena, The Big O, Record of Lodoss War, CardCaptor Sakura, Trigun, Cowboy Bebop, Crest of the Stars, Serial Experiments Lain, Rurouni Kenshin, Di Gi Charat, Excel Saga.
Whew, that should be it. It's early in the morning here now, so I've might missed a few titles. I wanted to type Gensoumaden Saiyuuki too, but then I remembered that it's from 2000s.