All what you have to do in this case is :
1- install lotus notes domino server on the new machine .
2- copy every thing from the old Lotus Notes machine to the same location in the new machine , and specially make sure that all the ( .cer) the (.nsf) the (server.id )and (notes.ini) must be moved to the same location (e.g. C:\lotus\domino\data)
* I think Lotus notes 8X and later are the only ones supporting win2008
* all ( .cer) the all (.nsf) the (server.id )and (notes.ini) are the most important ones to be moved .