AFAIK: No gui password prompt program is available for the N900 and thus that specific solution would require manual work in making one. The other possibility is you set yourself a user password (leave root locked unless you have specific reason to need it), and then completely change your sudoers file to prompt for a password in order to gain root.
sudo pwd
However, you would then need to go through and modify every .desktop file and have it launch in a terminal window instead of directly so that your terminal will ask for the password. Not elegant, and certainly not easy... not to mention extremely likely to brick the device unless you know exactly what you're doing.