I wish disneyland had Mickey's philharmagic, but unfortunately they do not. We enjoyed it so much we saw it twice in one day at hong kong disneyland so it isn't a WDW exclusive.
The muppets show "Muppets Vision 3D" at DCA is a good one for young kids. There's also a bug show "It's tough to be a bug" but i think a 3 yo would be scared unless he really liked bugs. My 9yo and 6yo watched it once a couple of years ago and they have no desire to watch it again.