Peter David's Captain Marvel run. Funny, cool, thought-provoking at times, and weird in the all right ways (not like Morrison's meta-on-meta commentary crap). He got a character that really no had before and while the whole "Captain Marvel goes insane" arc ran longer than it should it was always a fun read. While I do think giving Carol Danvers the Captain Marvel mantle was right decision I still like this version for it's absolute bonkers take on Marvel's version of Captain Marvel.
X-Factor by Peter David. David's original run on the series in 90s is about 12 issues but his return to the series was the best X-Book Marvel was putting out. Keeping the team on the sides through most of the crossovers allowed David to actual comment and be snarky about some of it. Plus he did a lot with essentially C and D list characters, he made The Multiple Man a leader on the same level of Wolverine and Cyclops, he finally had Shatterstar and Rictor come out of the closet, Monet came out as Muslim, Siren dealing with the death of her father (her reaction was understandable in the Marvel Universe), a false pregnancy, and her drinking problems. He did some great stuff with Reign, Polaris, and Havok, Pip the Troll was a riot, plus the book was a lot of fun. Even when David had a damn stroke he somehow kept up with the bi-weekly publishing schedule and the book was never late.
The Green Goblin a 12 or 13 issue run that debuted the often forgotten Goblin who tried to really tried be a superhero.
Nightwatch Marvel's version of Spawn was very 90s but I still have a soft spot for this series.
Blackwulf Angel Media's artwork is the thing I liked about this series.