Finder by Carla Speed McNeil will always be one of my favorites. It’s a beautiful work.
Usagi Yojimbo might be the one that has brought me the most joy over the years.
Bone, Elfquest, Strangers in Paradise, Concrete, A Distant Soil, Wandering Star, Xanadu (by Vicky Wyman), Hepcats, Mouse Guard, Akiko, Groo the Wanderer, Thieves & Kings, and countless others are all in the mix. I tend to like the more light hearted fantasy stories. The 90’s and the early 00’s were a great time for those kind of Indy comics.
Runners by Sean Wang was a great comic that unfortunately didn’t get the attention it deserved. Well worth tracking down if you can find it.