Me, I'd buy the busa....better price, lower miles, newer bike and you know the condition of the bike. Plus, the busa is a better all-'round bike for slabbing long miles. Plus it is competent in the twisties.....
From a strictly $ standpoint... the busa : $8600
http://www.kbb.com/kbb/OtherVehicles...48&YearId=2006
vs the R1: $7500
http://www.kbb.com/kbb/OtherVehicles...43&YearId=2005
..again, you know I look at these with an eye towards the $'s; so take it with a grain of salt. Just seems to me that the busa is a bike I could ride for a year or two and break even or even make a dollar or two.....