The instructions here get you most of the way. You can fix the error of “unable to open channel” on wminput by specifying the hardware address on the command line as shown from the hcitool scan output:
00:19:1D:A8:44:AB Nintendo RVL-CNT-01
Used as a mouse via pointing against IR sensor bar is pretty painful. I think you’d do better with the control keys instead – but haven’t gotten that for yet myself. I plan ultimately to use it as a remote for xbmc linux.