I've tried to change my Call waiting alert by SSHing into my iPhone using CyberDuck. The steps are as follows:

1. Record my own tone and save as a .caf file
2. Delete the file named ct-call-waiting.caf under system/library/audio/uisounds
3. Rename my tone with the exact same name as the original
4. Put new file in place of the original

Alternately I also tried making a winterboard sound theme. Nothing seems to work

Does anyone know how to make this work?