I'm betting that the threat from Al-Aqsa is a bluff. (At least I hope it is.) But if it is real, and they do have some sort of WMD, I'd stake that is was something biological. That stuff can be reproduced fairly quickly, if they aren't too concerned with safety. But to use it in a city, with an explosive dispersal system, wouldn't do too much. It just wouldn't spread far enough. If they were smart (Let's hope they're not), they would render it an aresol and load it in a rocket. Shoot it over a city, and the wind spreads it as it sinks. Even if it didn't kill a large number of people, it would have a huge terror factor. It would definitely provoke a massive retaliation against the group and any nation which harbors them. If the US gets involved, (god forbid) it might be the nuclear option. Depending on which nation harbors the group, we could be looking at WW III, with the widespread deployment of tactical nuclear devices. And if the US has what I think it does sitting in its arsenal, everything could go south really fast.
The only saving grace is that this is an extreme worst-case scenario.