For the general case, it is theoretically possible in the kernel, using the owner extension to netfilter. I can see the option --pid-owner on the man page of iptables on die.net, but it says it is broken with SMP :(
In my own system, a 10.04, there is no such option on the manual :( . So I believe we are out of luck this time ;( . Maybe there will be another incarnation of the --pid-owner option some time in the future. A gui on top of that would not be rocket science.
The first step must be taken on Linux itself and iptables.
As for more specific types of traffic, such as HTTP. There should be ways to make accommodations using proxies, but it probably needs some hacking because this use-case does not arise often.