I've never heard of an FTP server with any capabilities that are even vaguely CGI-like. I suppose you could (very) roughly approximate it by having a directory where users can upload a text file containing a request and a cron job which checks that directory for request files and, if it finds any, processes the request and writes an output file, which the user can then download. But I doubt you're likely to get much closer than that without using a heavily-patched server (and probably a customized client as well) to add the CGI-like features.