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.
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.