Maxauthority, the founder of the vimperator project wrote his thoughts comparing the two on vimperator's google code page (http://code.google.com/p/vimperator-labs/wiki/VimperatorVsPe...)
In general, it isn't much different, however, since vimperator version 3 it will start being much more different as vimperator is now trying to make the user interface as intuitive as possible while keeping the awesome modal controls from vim where as pentadactyl will still try to conform to vim.
Check out vimperator 3's design goals: http://code.google.com/p/vimperator-labs/wiki/Vimperator3Des...