Yes, plenty. Vast differences in audio hardware between all 3, for one.
Although curiously enough, all 3 DK's can be run on the same VIDEO PCB (back half of 2-board stacks). I have seen JR's with DK VIDEO PCBs, and DK3's with JR VIDEO PCBs. To run DK3, you need to jumper a RAM leg to the bank of 4 EPROMs (to facilitate addressing of the larger ROMs), JR I'm not sure if it requires anything. I'm frankly surprised this has not been brought up before, haven't found any info other than what I have gleaned myself. This is surely why DoubleDK boards are easily modded onto JR boards, and makes me wonder about the feasibility of a TripleDK run on DK3.... Not that I would consider running one (as with Double), but it sure would be cool.
/me scurries off to patent office