I'm in the same boat as everyone else here unfortunately
Late 2008 unibody MBP with screen flicker when "better battery life" option is enabled via Energy Saver. Basically when the 9400M is in use the laptop is borderline unusable at this stage; but I've put up with it for a little while.
From my perspective it seems unlikely to be a display issue as the issue is not present when the 9600M GT is in use. To me this (logically?) points towards either a hardware issue with the 9400M, some bizarre software/firmware fault, or a peculiar hardware fault elsewhere... but not the display itself. I can't be sure however! I'm no technician/engineer.
Anyway; I finally decided to try and pursue it via Apple Retail (local Genius Bar) myself after reviewing this thread every now and then over the last few months and seeing no obvious progress. As expected I wasn't really able to get anywhere - especially considering my laptop is also out of warranty. I was advised to use the 9600M GT, despite the significant decline in battery life (which is important to me as a student) and carry my charger around if this alleviated the issue. I referred them to this thread, other threads, and multiple other websites/sources and they basically just said they could check it out at my expense if I liked but didn't recommend "throwing money at it".
Apparently it is not a known issue by Apple however and I asked them to confirm this several times, which they did via their system and by checking with someone else.
I find it absolutely insane however that this thread, and issue, has been open for over 2 years without any resolution or acknowledgement of sorts. It seems Apple retail at least are unable to identify anything.
Is there an escalation path that can be followed? It seems no one has done this just yet from the looks of things... If one is outside of warranty, are they able to contact Apple via email/phone and well, politely, pursue escalation/acknowledgement/ensure someone takes ownership of the problem? Having a look at
http://www.apple.com/au/support/contact/ it doesn't really seem clear... almost seems like you're not eligible to contact Apple via the phone if I'm out of warranty/Apple care.