I don't have a single favorite one, so here is a top three, in no particular order:

Freefall The first webcomic i read, started in 1998 and still updating three times a week.

El Goonish Shive Another longrunner, started 2002 and still going. Helped me with figuring out some gender stuff.

How to be a werewolf Newest one on the list, starting in 2015, also still going.