I have a few favourites - the aforementioned "DUCK!" episode from Season One, the Christopher Reeve edition with Rowlf as the patient, the one from the Gene Kelly episode with the announcer crashing into the OR at the end, and the one from the Buddy Rich episode with Beauregard as the patient (after accidentally shocking himself while trying to fix the theatre lights).
But I think my favourite is the version from the Phyllis George "Muppet Awards" episode, in which Dr. Bob keeps reading his acceptance speech (especially after learning the competition for Best Sketch is "Pigs In Space") and the cast eventually shrugs and walks off after Miss Piggy, realizing she's in both nominated sketches, mutters "Not much point in going on" and eventually leads the cast offstage.
(The topper, of course, is that Phyllis George subsequently announces that "the judges have decided not to present an award in this category," infuriating Piggy.)