Just a couple of thoughts:
1) The Gigabyte motherboard is full length. That doesn't belong in a system that I believe you'd try to make it as compact as possible. Think micro-ATX / mini-ITX format (will affect / be affected by the case choice)
2) I can't pinpoint the case (for that price) so... the exact model please.
3) I didn't quite catch the argument with Vista and MPEG-2 decoding. For once there are better free alternatives (Gabest decoder, etc). Second, MPEG-2 is a shrinking part of the equation, especially when going Blu-Ray, so you'll have to think more about the AVC decoders and the likes (ffdshow, the filters in MPC-HC which are available separately too, etc, to stay on the free side). As for UAC that can be turned off (is still anybody keeping it on?!?!). Also keep in mind Windows 7 is around the corner (RC is available and good for ~11 months without any nagging warnings; you'll have some other problems with the codecs but they're solvable).
4) Media Center... what version?
5) What are your intentions for storage? Is this already addressed as some form of external storage / NAS / whatnot? 640GB for a HDD is neither here nor there. If it's just for boot I'd go with something smaller/quite/cheap/reliable. If you plan to store movies - we're talking TBs and we're branching out to something else (and significantly more money).
6) No mention of any kind of TV Tuner - what are you intentions there?