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.