I have a business user asking that I put links from our external site to our intranet with a disclaimer next to the link that it's for our company's use only. I've never heard of that being done. Does anyone do that? Does anyone know if any problem could arise from doing that, like spiders trying to follow the link and causing 404 errors; search engines getting confused etc..?
Just block it in your robots.txt and you should be fine. It's not uncommon for sites with clients or partners to feature a section especially for them. For example, many manufacturers have special sections for their partners to come download marketing material and read about upcoming promotions.