*****Season 5 Spoiler Alert!!!*****
Arguably the funniest short bit they ever filmed ever was when (relatively new father) Martin mistaken takes the wrong baby. It is from Season 5, Episode 2--"Dry Your Tears," first aired on September 19, 2011). The segment occurs about 42 minutes into the episode.
Set in the Portwenn Surgery, an attractive young woman in the waiting area is seen attempting to comfort what we are meant to assume is the mildly fussing baby James Henry. Louisa is seen descending the stairs in the background, presumably to fetch her offspring.* The as-always flustered Doc enters from his examination room and brusquely takes the baby from the surprised but silently acquiescent woman (actress Christabel Muir, I think).
As the patient-mother looks on in (confused) silence, Martin and Louisa retire back into the Doctor's examination office, where Martin attempts, unsuccessfully as always, to inoffensively chastise Louisa for some perceived (by him) problem with the way she is performing her (temporary) role as receptionist. Louisa is having none of it, naturally, and retreats back into the waiting area.
As she leaves, Martin (who has lost his initial argument) pleads, "Louisa. Could you take the baby, please?"
Louisa responds, triumphantly, "That's not our baby."
The perfect comedic double-take performed by Martin Clunes and the anxious look by silently-suffering young mom (Muir) in the waiting area are priceless.
* Viewers (especially men) who understandably fail to spot the comedic "sting" approaching can be forgiven since producers used several different children to stand in for Baby Ellingham, and the timing of the whole rapid segment is brilliantly set up, executed, and edited.
Addendum: Runner-up for best quick gag is Morwena (Jessica Ransom) fainting dead away at the sight of an injection needle, in Episode 5 of Season 5.