If you're planning on doing anything on IIS, besure you have the patch cluster du jour or prepare to have your box turned to swiss cheese.
Personally, for a file store, I would use ftp. With http you have to have the security on the server set up, then you also have to worry about the browser's security. Ex. Mozilla, IE, and probably a bunch more save passwords. If you go to some cluster (pure guess that you're at a university here) or someone you gave access to clicks the save password button, you just lost whatever security you had set up, even if it's 24 bit encryption, or 2billion bit.
Ftp it's (almost) all in the server. Just make sure you don't run an anonymous or use wu-ftp on a *nix. There's plenty of other issues but that's my .05 (inflation dontcha know)