Some collected tweaks to Apple Mail.app:
- Force Mail to display plain text by default
- Apple KB: Mac OS X 10.3: Mail – About SSL, IMAP Accounts, and “Remember My Decision”
- Adding a custom SSL Certificate
- GPGMail – works great for me, does S/MIME, I use it with MacGPG for key management
- Apple Mail Resource Page – great list of add-ons