This seems awfully like speculation, but for everything motorcycles are supposed to do, including all the intangibles like elegance, sound, and mystique, nothing approaches the Italian machines. However, they are expensive, easily three to four times the price of Japanese iterations.
So, you got forty thousand dollars? The Ducati is a true homologation bike and is very near perfection. It is actually 1199cc in displacement, comes with a slipper clutch, traction control, data aquisition (for laps), and makes 180hp. And remember, all of this is from two cylinders. A few thousand less will get you onto what many consider the sexiest bike made, the F4, an in-line four but nothing like its Japanese counterparts. Again, heritage, sound, and rarified membership are customary with this maker, too.
If your bank account is not so stratospheric, the bike of the year was won by Honda (2008); their litre class machine beating out the other three marques from that country. Yamaha, by the way, despite looking so good, came dead last as it has not seen any design changes in five years and suffers mid-range lag that simply puts it out of the competition. The GSXR was a close second, and might even had won had it not already won so many times before.
So, best buy for your buck? The CBRR 1000 from you local Honda dealer. It comes in red, too.