Squid is a HTTP/FTP proxy. POP and SMTP are not http protocol.
I imagine you want to set up a secure channel to send your POP and SMTP traffic through.
If you want to use a proxy to allow POP and SMTP through secure channels (so that the man in the middle cannot sniff your data), you'll need something like a SOCKS proxy and SSH Tunneling.
I've found this document that might be usefull:
SSH Tunneling and SOCKS
It might also be usefull to read this: