It all depends on what sort of segment the packet source and sink are on, and the types of stuff you're doing in the middle. If all your hosts (servers and workstations) are on 1500 byte mtu segments, and you're not doing anything "special," then you don't really need to bump the mtu's in the middle. If, however, you are running tunnels, encryption, mpls, or other type sof things that are going to generate larger packets through the middle of your network, then bumping the mtu is really nice.
It could also make a difference if you're converging BGP, and would like to reduce the packet count across the wire. EIGRP won't transmit anything larger than a 1500 byte mtu no matter what the actual mtu is, so you won't get much help there.... IS-IS, I think, can operate over jumbo links, reducing packet count, but I'm not certain cisco supports it, or what happened to the drafts on that one. OSPF, I think can take advantage of larger MTU sizes, since LSAs are repackaged at every hop, anyway, so it might get some gain out of larger mtu's.
Hope that helps....