After some research and trying a bunch of stuff that didn't work I figured out that you can get this to work on Ubuntu without installing anything!
Just use the default remote desktop server (vino) in
System>Preferences>Remote Desktop
Check the boxes to 'Allow other users to view your desktop' and 'Allow other users to control your desktop'. You should also definitely set a password. When you click the 'Close' button the server will be running.
That's it! Just go into the Touchpad app on your iPod/iPhone and add a new server with the IP address of your Ubuntu computer.
The key there is to enter the ip address with NO port number because vino defaults to zero as the port number. You will get a message that the 'Connection Failed' if you enter zero as the port number. Use the following settings (as described with screenshots on the Touchpad Pro website
Touchpad Pro: Touchpad Pro > Setup > Windows )
Name: enter a friendly session name
Address: enter your local ip adress with no port number (ie. 192.168.100.69)
Password: enter the password you set in vino
ScreenView: turn this off unless you bought the ScreenView upgrade
Mac Mode: turn this off
Media Server: turn this off (this only works in Windows)
Connect by tapping the new entry with your friendly session name. You will see a message on the Ubuntu screen that a remote user is connected and the iPod/iPhone will go to a black screen that acts as the touchpad and the buttons at the bottom will bring up the keyboard if you need it.
I haven't purchased the screen view so I don't know if that works but the mouse and keyboard are flawless. I really just tried this for novelty but if I end up using it a lot then I'll pony up for the advanced features. I also have not tried connecting from a different network or without wifi. If anyone else tries the advanced stuff I'd love to know how it works. I am using an 8gb iPod Touch with 1.1.4 firmware and Ubuntu Gutsy on a MacBook.