some more i remembered:
American Born Chinese by Gene Luen Yang. Three separate stories that connect towards the end, exploring Chinese identity, stereotypes, and especially in relation to the Chinese diaspora and growing up Chinese American.
Fun Home by Alison Bechdel (creator of Dykes to watch out for, where the Bechdel test comes from). A memoir about her childhood, especially her relationship with her father.
And I kinda gotta mention the Sandman by Neil Gaiman. Not really sure it counts as indy, and it isn't exactly a hidden gem, but it's in my top 3. There are 75 issues of the original run, collected in 10 volumes. Morpheus, the titular Sandman, is one of the seven endless: Death, Desire, Despair, Destruction, Destiny, Delirium, and himself, Dream. There's several different disconnected stories, sometimes with an overarching plot.