uuummmm
I have heard this on may be one or two of the flights I have been crew on. It came from the flight deck and on both occasions it was after a particularly difficult flight.
It was appreciated by me and most of the crew. I would personally say that if it is a run of the mill flight then it isn't really needed, but after a problem flight it can sometimes be nice to be thanked by the PIC. After all all we want to do when we get to the crew room is get the hell home usually.
Sometimes I've even known the PIC not to come up to the crew room.