For the CPU on my Jornada, I have 3 options for Mobi Reader: 4.8, 4.9, and 5.3.
4.8 is the Mobi Reader recommended for WinCE devices. It works okay. Be sure you go get the free registration code so you can keep all the features.
4.9 doesn't seem to have any extra features, but I use it because it works just as well.
5.3 doesn't work completely because it is intended to run on Windows Mobile, and I lack the support files needed to display menu bar properly. It still mostly works, though.