Hiya
I see someone has already posted a list of the discs that will fit, but if you are going down the route of swapping to the R1 Blue Spot type Calipers, most of the Yamaha Discs will not get around the problem of Clearance.
The issue you see is that the Blue Spot Pads run deeper on the disc(ie the inside edge of the pad is closer to the wheel spindle and therefore fouls on the standard YZF (FZR etc) disc mounting buttons (the rivets that hold the discs to the centres).
R1, Thunderace etc discs will not swap as the disc mounting points to the wheels are different.
Therefore you have 2 real Options:
Option 1, re-use the original discs and just remove a little pad material to clear the disc mounting buttons..(check the condition of your discs though as the standard 6 pots have a habit of warping them and there is no point upgrading the calipers if your discs are still warped)
Option 2, Swap to the Ducati, Aprilia (or later Yamaha XJR possibly)(the mounting buttons are apparently different on these so the clearance is not an issue).
When I say make sure your pad material is matched to your discs I mean make sure the pads you use are compatable with the material the discs are made of and for the type of riding you do, sintered pads for Steel, organic/ceramic compound for Ductile Iron (like my PFM Discs).. Track pads do not suit road riding and vice versa...
Finally go for the best set up you can afford, but match the parts wherever you can.
Hope that all makes sense
Andy