I've always been a fan of Gilligan's blend of the deeply personal/serious while filtering a wry ironic tone throughout... he dances with the absurd. He can create a lot of empathy and pathos for protanogists simply by the terrible luck they all seem to have, and yet it never really drops into farce, they all still seem like very real people.
He had a bit of "quirk" even in his first really famous X-Files episode he solely wrote (Pusher -- there's a weird emphasis on the color "Cerulean Blue"), but "Small Potatoes" was probably his first great example of an episode that was quirky at core while still being able to take seriously, and involved some scrutiny of Mulder, having him question why he could have so much going for him and yet (at least in society's eyes) end up being pretty much a loser.
He worked with Michael McKean in the two-part "Dreamland" there (first time working with him?), which was more a comedic episode (with Nora Dunn as McKean's screechy wife who Mulder has to deal with since he and McKean have switched bodies temporarily). But in "Hunger," he takes a really crazy idea (the fast food worker who is kind of a human shark and is trying to kick the habit of eating people) and explores it horrifyingly to its ultimate conclusion; so much of the episode can make you laugh at its approach to 12-step programs, but at the same time this soft-spoken person is wrestling with who and what he is, and the end is rather shocking in its existential bleakness. You see also his first directing attempt on X-Files (plus writing) on Je Souhaite -- the sardonic genie who enjoys twisting around the wishes of supplicants who free her from her magic rug. You can just see him practicing this "tone" of his that ended up being a mainstay of Breaking Bad and now is channeled into Better Call Saul.
There are similarities to BB and BCS, but so far BCS seems to be a bit more light-hearted in tone even with some serious elements.
