Well, the Sony VGX-XL systems were the top of the line of Sony computers, and today still retain their own unique fashion... in particular, I like the fact the cabinet is like other hi-fi/video rack devices (19'/43cm), so it fits in any audio/video system without to be "out of place"; also, its wireless keyboard is small, and with integrated touchpad; it could be used "out of the box" to capture analog audio and video, and, as I discovered years after I bought my first one, it could be upgraded to be really much more powerful than it was at factory default.
About CPU: the motherboard does not allow overcloacking, and even if it will with a BIOS upgrade, I'd like to leave its frequency at factory default, to prolong its life; as you wrote, it's quite difficult to find a brand new Core 2 Quad, and the used ones were almost all overcloacked; this is why I still use my old Core 2 Duo.
About GPU: I'm pretty sure it will increase a bit the speed, even if I agree it will be not comparable to the cost difference; but, as you know for sure, when you upgrade your PC with the best CPU, the biggest HDDs, the fastest RAM your mother board allow, why you shouldn't do the same with the GPU? (^^,)
About RAID: can you confirm that, if I buy two identical SATA HDDs, set them to RAID0, plus another SSD for OS, the speed improvement will be 40%? I mean, if virtualdub process an avisynth script at 10fps before, it will be at 14fps after?
Well, here you are some info about the VGX-XL system:
http://reviews.cnet.co.uk/desktops/sony-vaio-vgx-xl202-review-49285076/
http://web.archive.org/web/20130626000943/http://store.sony.com/p/VGX-XL1/en/p/VGXXL1 (technical info on the less powerful model, just to have an idea of how much ahead of its time it was - released in 2006)