dvduval - 2:32 am on Aug 15, 2010 (gmt 0)
If I interpret your question correctly, you are wanting to know if a particular script or software would lead to google treating the site differently. I would say the answer is most certainly "NO". There have been multiple occasions where people like Matt Cutts have expressed this. The only caveat would be if the software violates the google terms of service.
I would be wary of things like bidding directories that are created for the sole purpose of buying and selling pagerank, or any tools built for directories that would query the google servers in an unacceptable way (ex. trying to get the pagerank of 10,000 links updated).
It doesn't sound like you have any intentions like these, and I think there are a number of different script you could use that would be just fine.