Depends on your mail provider. Our school email system offers a secure web portal for remote mail access. For those who prefer downloaded mail (POP), we use the secure POP (POPS) version.
Online web mail services like Yahoo! have secure log-in facilities, although I think the rest of the session isn't secure.
If your provider offers it, I'd avail of using the secure versions of the mail protocols (POPS or SMTP/SSL). Worst case scenario, you can always just do a secure SSH tunnel.