Given how big some of the MIME parts can be, I prefer not to keep copying them around. People mail around video clips and presumably some day will do the same with entire movies.
We treated MIME as a wire protocol and converted the directory tree to a MIME stream at the last second before transmission and applied a content-transfer-encoding if it was going out via SMTP (we had an alternative protocol, RSMTP, that didn't require encodings).
