To configure my Kingsis Peripherals Evoluent VerticalMouse 3, I've added the following fdi (HAL configuration info) to
The most important part (for me) here is ButtonMapping: by default only the wheelbutton triggers middle click, but since it's rather hard to press (and I use it often for pasting), I've mapped it to the middle button on the right side, too.
Also, the thumb button becomes "Back" (in browsers) and the lowest button on the right triggers the context menu.
Update: This was meant to included in Ubuntu Karmic (see bug 451729), but then got removed again (not everybody liked it).
Update^2: for udev (which is used solely since Ubuntu Lucid), I've transformed it into the following file (which you can store as
(see also https://wiki.kubuntu.org/X/InputConfiguration for more information)
Update^3: This is bugged in Ubuntu Lucid.