1. 'The Time Traveler's Pig' (Season 1, Episode 9)
This was the episode that made the grand design of "Gravity Falls" crystal clear. In the episode, Mabel attempts to win a pig (beloved fan favorite, Waddles) at the fair, while Dipper attempts to not screw up his flirty interactions with Wendy. The twist (since there is, of course, a twist) is that Blendin (voiced by "Rick and Morty" creator Justin Roiland), a time agent, has also come to the fair and his time device will allow Dipper to correct his mistakes but potentially cost Mabel her pig.
This is perfect "Gravity Falls" material, but what made the episode so special is that it periodically visited moments from previous episodes and, if you watched those first few episodes (including the pilot) later, you'd see those same disturbances. (If you were particularly eagle-eyed, maybe you noticed the first time but just weren't sure what they were.)
The only thing better than the time twisty stuff (directed by series MVPs Aaron Springer and Joe Pitt) is its emotional resonance. It was, in short, a mind-blowing revelation and clearly cemented "Gravity Falls" as the smartest and most fearless show on television ... that just so happened to be on the Disney Channel and Disney XD.