I've only had it happen twice so far, but I've just started using OmniGraffle. Both times that it occurred, I was using Graffle at the time and experienced the exact same set of circumstances you mention. My 2 events happened about a week apart, and during the intervening time I had no problems though I use the laptop heavily. Also, I see the same thing in the system log:
Mar 31 10:54:32 Macintosh-4 kernel[0]: NVChannel(GL): Graphics channel exception! status = 0xffff info32 = 0xd = GR: SW Notify Error
Mar 31 10:54:46 Macintosh-4 kernel[0]: 0000000c
Mar 31 10:54:46 Macintosh-4 kernel[0]: 00200000 00005097 0000047c 00000000
Mar 31 10:54:46 Macintosh-4 kernel[0]: 00000486 00000f04 bfff7ff4 00000003
Mar 31 10:54:46 Macintosh-4 kernel[0]: 00000000 00000000 00000002
Mar 31 10:54:46 Macintosh-4 kernel[0]: 0000000c
Mar 31 10:54:46 Macintosh-4 kernel[0]: 00200000 00005097 0000047c 00000000
Mar 31 10:54:46 Macintosh-4 kernel[0]: 00000486 00000f04 bfff7ff4 00000003
Mar 31 10:54:46 Macintosh-4 kernel[0]: 00000000 00000000 00000002
Mar 31 10:54:46 Macintosh-4 kernel[0]: NVChannel(GL): Graphics channel exception! status = 0xffff info32 = 0x3 = Fifo: Unknown Method Error
Mar 31 10:54:46 Macintosh-4 kernel[0]: 0000000b
The last 2 lines repeat about 40 times until I power-cycled the laptop. Perhaps it's time to figure out how to submit a trouble ticket to Omni?
Dan
ps Should mention I'm on a MacBook Pro running 10.5.2 as well