Halogen free PCBs still aren't that common and all of the bugs aren't worked out of the systems yet, but they are starting to show up here and there. I suspect that like RoHS a few years back, we will be seeing more and more as time goes by.
If you do feel the need to try out a Halogen free PCB, our experience here suggests that they are more sensitive to moisture than standard FR-4 and are a bit more brittle. That might be an issue when de-panelizing boards or when putting a lot of mechanical stress on a pcb.
An article in "Future Circuits International" suggests that some of the replacement flame retardant chemicals may have other environmental risks too, but I guess that seems to be the case with just about everything we pull up these days to replace something that is a known hazard.
Anybody with some good practical experiance here, feel free to chime in.
No matter where you go, there you are