Scooby-Doo: Mystery Incorporated is very much like Gravity Falls. Both start off episodic, with clues scattered here and there, and build up to an apocalypse. (The show is even better if you grew up watching, or are familiar with, any of the other Scooby-Doo shows.)
For a show with dark humor, I recommend Invader Zim.
Also agree with others about Over the Garden Wall, Avatar: The Last Airbender, and Korra.
For current shows, We Bare Bears is pretty good. For zany humor, I like the Amazing World of Gumball.
On the live action side: Buffy, Angel, and the X-Files. I also think Sleepy Hollow has a Gravity Falls vibe.
And if you want more Sherriff Blubs and Deputy Durland, you might want to check out Psych. The main characters, Shawn and Gus, have such a close and weird friendship that people think they are a gay couple.
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