I've only done it in fic once, which is odd considering most of my fic takes place S4/5. But in "Black Satin Voices," D'Hoffryn authorizes Halfrek to use her powers to remove Spike's chip hoping that the lack of a tether will make him attack Buffy (and stop Buffy from making trouble). She pretends to be Cecily to gain access to him when he's sick and magics the chip out of his head.

Oh, and Spike's chip doesn't work on occupants of the painting in "Rhapsody in Oil" but I used the excuse that it was because they were part of another dimension. Does that count? :)