I'm currently running my pfsense on a via mini-itx board with dual nics.
I only have one pci slot available so my question is if just one INTEL PRO 1000 GT will increase my thoughput?
As it is now I have only a throughput around 60mbit on my 100mbit connection.
It will to some extent, but not as much as replacing all the NICs. The Intel cards do more on the card and require less of the CPU. Since it sounds like you're maxing out the CPU, replacing one of the NICs will lower your CPU usage (or allow you to push more traffic before pegging the CPU). But not nearly as much as replacing both would.
I'm not sure exactly how much benefit this will provide since you can't replace both NICs, but it should have some measurable benefit. If you try it, let us know how much more you can get through the box after doing so.