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Shaenon Garrity's Skin Horse is a bit of an odd duck here— it was the spiritual successor to Narbonic. A group of misfits providing each other with emotional support; one or two non-human sentients trying to find a way to fit into the world; and a dash of UST. Now, however, a Narbonic character has made an appearance in Skin Horse, promoting it (retroactively?) to actual sequel.
It's been confirmed by Word of God that UNITY is what the military did with the samples of Mell's DNA that Helen sold them. If that wasn't planned from the start it fits together very neatly.
Girly by Josh Lesnick is... kind of a Spiritual Successor to his previous webcomic Cute Wendy. The two main characters from Cute Wendy are the mother and father/mother of Winter from Girly, but the stories are separate and unique enough to be considered a league of its own.
Three Panel Soul is the Spiritual Successor to Mac Hall. The relationship between the two comics is not dissimilar to the relationship of one's life during college, and one's life after college (and not without good reason, either, since that's what they're about with regards to Matt and Ian).
anti-HEROES openly acknowledges right at the top of the page that it was inspired by Rich Burlew's The Order of the Stick, and uses a similar stick-figure style as well as medium-aware gags, and even a few breaking-the-fourth-wall-references to Burlew's style. The overall plot and universe differ significantly, though.