I can attest the Aqua version of SAOImage DS9 version 5.3beta does indeed play nice with Apple’s dopey firewall behavior (see here for notes on version 5.2’s incompatibility with the Leopard firewall). However, the command line version that uses X-windows DOES NOT play nice with the Leopard Firewall. If you run the X-windows version of “ds9″ on a Mac running Leopard’s built in Firewall in “Set access for specific services and applications”, you will end up with a completely hosed ds9 executable which will not launch ever again.

As such, for now, since I prefer the X-windows version of SAOImage DS9, I am leaving the the Firewall off for now, I’m not too concerned.