Not a perl/webserver solution; but, is there anything stopping you from just using ssh to access your files? Since you seem to be particularly paranoid, you could use s/key one-time passwords. That way it doesn't matter if there's a keylogger or if someone sniffs your password. It's also way more convenient than carrying around a CDRW :).

You can download putty from anywhere to get access.

That said, basic http auth over ssl strikes me as being properly careful, unless the data's super sensitive.

Update: Touched up a little.