Intel is ahead of AMD right now, but I don't think you'd notice a huge difference between the two unless your encoding or constantly using 100% of the processor. (Also, most applications are just being designed to handle 2 cores, so right now you won't notice a huge difference between 2 and 4 cores) The Q6600 is really popular right now and seems to OC well up to 3.0Ghz+. Of course, just upgrading the CPU won't boost the performance in games unless you have a newer graphics card (8800GT s/x or the 2900)
Yeah, your GPU is getting bottlenecked to the performance of a 7800 or lower with that chip. At least, that has been my experience. Upgrade to the Quad and you should see a world of difference in games.
Also, what PSU are you using? Make sure it can handle all your stuff together.
I hate to say this but even a Q6600 has a hard time running supreme commander, so don't expect blazing speeds. I have this game and a 8800GTS 320mb can not play all the setttings on high smoothly. I overclocked my Q6600 to 3Ghz, and it helped some during late in the game where everyone has 500+units. You also need A LOT of ram. IF you run Windows XP, each program is limited to 2gigs, so even though you may have the maximum supported 4 gigs, Windows XP limits each program to 2gigs. This is a huge problem because when playing on larger maps, the 2gig limit is reached and your computer crashes. This is a very common problem for us Quad people, since people with Quad cpus wants to play big maps with many units. I had to page 4gigs of my fastest HD to satisfy the needs of Supcom, and even with that, it's still crashes on large maps.
I can't say from personal use but people are saying new updates are smoothing out the performance with Vista. I think in the long run you will be better off with Vista so you can utilize more memory and truly play direct x10 games.
This will be my next move but it will be done as a dual boot. I can't see completely giving up XP anytime soon.