I cheated when answering:
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I've found that most sit-coms in the last 10 years have had one or two seasons of greatness (or greatness sprinkled all the way through.
So, picking only one? Nope. But …
Arrested Development (2003-2006) is the master of the gradually building running gag.
Community is inventive and has the bonus of pulling back the curtains on how a sit-com works. Not only about the plot mechanics, but about watching a team of amazing writers correct the faults it discovers in the show as it's running. It needs to be heavily curated though. I'm happy to point you in the direction of what I consider to be the 'right' episodes to watch. The creator, Dan Harmon, has also done great in-depth interviews with the AV Club and Alan Sepinwall that make great companion pieces.
The Thick of It (Season 3) combines humanity, astute observations about how political power is wielded and lost, and is pretty damn filthy.
How I Met Your Mother (Seasons 2 and 3) are a show coming into its height: most episodes play around with narrative structure or running gags. It also has a lovely rom-com heart.
Louis (Season 2) is something I haven't seen, but reliable reviewers have described it as incredible.
Silicon Valley (only one season so far) has the setting with the most comic potential of any sit-com I've ever watched.
Personally, I've also found Big Bang Theory has executed its premise splendidly. It's trad multi-camera comedy, and one day I will write my defence of it—but I have found (a) that by turning geeks into the lead characters, the first few seasons found an entirely fresh field of jokes to plough, and (b) despite massive stumbling blocks in Seasons 3 and 4, it fulfills the promise it makes to the audience and is not afraid to let its characters grow. The latest season I've watched (7) is disappointingly filled with misogyny and jokes about obesity: some episodes were basically unwatchable as a result.