I have a .wav file... this I export from QuickTime to aiff format, then rename extension to .caf.... then I remove the original new-mail.caf from the /UITones/ directory and upload the new file. However, the file does not play-back when I receive a new email... if I replace it with the original, it plays... the .caf file plays nicely on my Mac....
If you have Cydia installed, install OpenSSH, and install Customize. SSH into your phone, and go to /private/var/mobile/Library/Customize2/ Create a folder as a theme. Title it Mail Sent Sound, or whatever you want. Inside that folder, create another folder entitled MailSentSound. Put the file in that folder on your phone. Completely restart your phone. Go into Customize, and change the MailSentSound to your newly uploaded one. Good luck!