I agree, I think it is a GPU issue.
To anyone not having this problem, try this for 15 minutes.
Download any 720P h.264 video from Apple.com/trailers
Play the movie and under the view menu, choose loop, to get the trailer to play over and over again.
Open two terminal windows and type this command in each.
yes > /dev/null
(this does nothing more than drive processor utilization to 100%)
Ok, I was interested in this issue and did the procedure.
1) First looped Speed Racer 720p trailer for 30min. Some programs running in the background (Azureus downloads, Safari). No stutter in video, cpu temp in the 60-65 range. Cpu utilisation about 50%.
2) Added the "yes > /dev/null" windows, maxing out the processor usage. CPU temp raised to 85C max, then settled back to around 75C. Kept this running for over half an hour. No core shutdowns (according to activity meter on dock), no stutter or noticeable frame drops. EXCEPT FOR: When Time Machine did it's hourly backup, the video playback dropped frames and stuttered occasionally. After the backup completed, video did run smoothly.
So, if I'm ever going to have an occasion where I need to simultaneously do some heavy calculation AND watch an HD video on my Air, I should turn off Time Machine. I guess it is a system process and takes precedence over user processes like Quicktime, and this causes the stutter.
YouTube videos take up about 40% CPU, which is only a bit less than 720p Quicktime! Last night I watched a 1.5GB DivX movie in VLC player which took only 20% CPU, and the fan kept silent all the time.
My MBA is 1.6 & 80, week 07 model. The only problem with this unit is a fault in the display panel (light spots "burn" momentarily on the screen), and I'm a bit afraid to take it back.. Will they take it in for a month to repair (I would miss my baby!), or will I get a new unit with possible overheating problem? Fingers crossed.
I really hope you get your overheating issues solved, and hope that my experiment was helpful.
Edit: I don't have an external display or TV, so couldn't test with them.