Out of the box, the Pre does not support self-signed certificates for email (and maybe other purposes).  There’s no simple way to make it work, but based on piecing together various threads on discussion boards, the following process seems to work:

1. Get a copy of your certificate (not the private key, but just the certificate).  I used openssl s_client mode to connect directly to my mail server for this.
2. Convert your certificate to DER mode if it isn’t already (maybe not needed).  I used openssl x509 mode to do this.
3. Plug in the Pre in disk mode.
4. Create a directory called “certificates” on the Pre.
5. Put your new certificate in there.  I used a .crt extension, but maybe others will work (e.g. .pem, etc).
6. Eject the Pre.
7. Go to the “Device Info” app.
8. Choose “More Info.”
9. From the menu, choose “Certificate Manager…”
10. Hit the plus button and select your certificate.  You’ll have to go through the warnings and you can verify that it contains the info you intended.
11. Return to the email setup and try again.