TCS and GeoDis are the programs to use for NCA, but recently two programs came out that automate NC inference: AUTOINFER and ANeCA.
Addendum (30 Oct 2007)
Panchal & Beaumont (2007) of ANeCA report that Ai-bing Zhang of AUTOINFER has noted that there are some issues in the program that require resolution and that it has temporarily been withdrawn.
notes on evolutionary biology papers/programs and other stuff: a non-frequent approach