if you have Appletalk users throughout your enterprise, and IPX users throughout your enterprise, there is almost no point in broadcasts from one group being visable to the other group, they are unlikely to be useful. by building VLANs based on protocol you reduce traffic in each group without reducing the flow of information.
LAT, DECnet, Appletalk, and IPX are all on the downturn thankfully, but not gone. protocol based VLANs support them gracefully until they mature away. I tried to remain child-like, all I acheived was childish.