May 2010 I took my Late 2008 15" unibody MBP in to the genius bar because it wasn't waking from sleep. They replaced the logic board and suddenly this problem started for me. It is exactly as described in the post and the comment by Bob above. I lived with it for 4 weeks and then brought the laptop back. They replaced the logic board again and it didn't help. It seems like there is no fix at this time. I booted off a clean install of 10.6 and the problem persisted.

There is a thread at Macrumors that implies that "Apple engineering is aware" but no definitive solution has been found.

MBP has two graphic cards
Higher Performance setting uses the 9600M GT card
Better Battery life uses the 9400M card

Screen Flash/Flicker happens exclusively on the 9400M card. Video out via mini display port running on the 9400M card does NOT produce this flicker, tho.
Flicker happens randomly – more frequent occurings when stressing the gpu out, letting the MBP heat up, using different angles or not connecting it to a power source can not be confirmed definately.
Flicker comes in three sizes in my case, about 1/5th of the upper half of the screen, about 1/3rd and a large one of about 3/4 of the whole screen.
Most of the time the flickers occur roughly on an hourly basis with some hours in between where you'll get around 2-3 flickers. All in all so randomly that some days you'll get a few work hours with no flicker at all and others where you'll get the 2-3 flickers within the first hour.

I had my logic board replaced for overheating issues with the 9600M GT card as the MBP froze from time to time. Not sure if I already had that flicker problem at that time but after the replacement I started to use the 9400M card more often and became aware of that flicker problem.
Brought it to the store for repairs a few weeks ago and they replaced the logic board again (for free after 1.5 years w/o Apple Care).
Problem still not solved, even tried a clean install two days ago, confirms that it probably ain't software related.

And to top it off, it seems my dvd drive wont work after the dvd drive update back in sept.

[first generation unibody]d

Recently experiencing some flickering problem when the MBP wake up from sleep. Very annoying…

Thank you for chronically this issue, hopefully we'll see it fixed

Anyhow, now I know about the "Higher Performance" setting workaround. That should help them fix the problem. But at least I get by through my next round of deadlines. Either way I will give them a heads up that the problem was not fixed.