I'm experiencing the same thing on my "first gen" unibody (Late 2008) 15" MacBook Pro.
After reading here, I realized I've been using the integrated 9400M chip for a while since I've been traveling and was willing to trade a bit of performance for battery life. I switched to the 9600 "card" and the problem doesn't show up.
Called Apple Care, got a very helpful rep, Thomas, who suggested starting by resetting the SMC - doing so actually caused the machine to boot up using the 9400M, and the problem immediately exhibited itself again (it seems quite random, it will go DAYS not blinking but other times it will happen every couple of minutes or even less than 30 seconds apart, quite infuriating). He suggested as standard troubleshooting to do an Archive & Install or a Clean Install - it just so happens that I'm swapping in a 500GB 7200.4 Seagate today anyway (the non G-sensor one, ST905003N3A1AS-RK aka Retail Kit version of the ST9500420AS).
I'm going to operate on the assumption it's a bad 9400 / logic board as I can't see this being software related, I've done a clean install and have had this issue since 10.5.6 but I can't blame the support rep for following standard procedure, especially since they were very willing to setup a repair/replacement if I called back and it was still doing it after the clean/re-install.
I just hope that the new board doesn't do the same thing, it would seem they have NOT fixed this issue in hardware yet, I wonder if it's somehow related to the poor manufacturing quality issues Nvidia had before (aka
http://arstechnica.com/hardware/news/2008/09/nvidia-sued-over-notebook-gpu-failu res.ars etc). Lets hope not!