To answer your question, it depends. Google will crawl some CGIs, but alot of it depends on exactly what your URLs look like and how much PR you have. The more PR, the more lenient googlebot is.
Hmm... so then is there really a point to me adding a cgi reciprocal links program to my site if google wont "honor" it? Are there other reciprocal links programs out there that arent .cgi and google will honor it? Thanks