As to whether you choose an isolated supply or not really depends on the device you're building. If no other equipment connects to your device, you could use the non-isolated solution, whereas if other equipment does connect, say like a serial to ethernet converter, you would want some isolation to avoid any stray earth loops via the piece of equipment connected to your device via the PoE and back to the PoE power injector. This can also depend on the Poe power injector as to whether it has an isolated supply for each cable. Unfortunately, I haven't looked at any commercial PoE power injectors or investigated the PoE standard to know what is 'standard'.

I've been looking at buidling some products using PoE, so if anyone has some more experience, I'd like to hear it also.