Best HTPC setup

You definitely did your research and covered all the basics. All the hardware/software setups you mentioned should be able to do the job. Most of my experience is with aio setups.

WAF and software support on the mythtv box are valid concerns, most casual users will find mce/v more appealing. I wouldn't expect a huge performance difference between either OS when using a decent CPU and GPU. A good 120mm HSF takes care of CPU noise and most video cards can be reasonably silenced. Storage can always be networked, but a couple low noise 500GB-1TB drives wouldn't be too bad.

I'm only using an A64 3800 X2 and 7600GT on my general use HTPC, but it's handled everything pretty well. The main tasks are HD/SD satellite via PCI DVB, DVD/CD ripping, and mpeg2/xvid downloads. Haven't tried much h.264 yet. Using Windows for my preferred DVB software and a few other apps/games.