I’ll go first.
Winner:
Breaking Bad, season 3 episode 10, “Fly”
Honorable mention:
Community, season 3 episode 10, “Cooperative Calligraphy”
PS: I’m having a hard time categorizing these as real bottle episodes since they don’t feel cheap or “fillery” at all, but they are at least spatially and plot wise confined.
Doctor Who reboot, season 3 episode 10: Blink. Minimal Doctor action, great villain and introduced Carey Mulligan to mainstream audiences.
Midnight, from a few seasons later, is my personal pick. The Doctor is there the whole time, but he’s just stranded on a bus with a few strangers. Great example of that “nothing is scarier” type of horror.
Blink is great, but it is not a bottle episode.
Edit: I stand corrected. Abed led me to believe a bottle episode happens in one place, but it’s any episode designed around minimizing cost.
https://allthetropes.org/wiki/Bottle_Episode
Which was still not Blink. Blink was designed to allow two episodes to be shot simultaneously but it is not a bottle episode. It uses new locations and new characters (almost exclusively, even)
Reading the Wikipedia page for Blink, I can’t see any justification whatsoever for calling it a bottle episode. I assumed from the upvotes, people knew something I didn’t, but, no, they just liked the episode so they upvoted the comment.