Dual socket boards require registered ram which is much more expensive and is slower than unbuffered ram, and require more expensive lower clocked CPU's , and offer no overclocking abilities. For your stated purposes a single quad system will be faster and much more economical. The only thing that would benifit from more than 4 cores is video encoding and the increased performance from 4 > 8 cores is not great and definately not worth the expense.
FB-DIMM is more expensive than vanilla DDR2, but not hugely so. Just don't buy the RAM from your OEM!! 4GB (2x2) of FB-DIMM is ~$140, whereas 4GB of DDR2 is ~ $80. This seems like a big difference, but DDR2 is just stupid cheap ATM. $140 for 4GB of ram is perfectly reasonable IMO.
Also LOL at the video encoding comment. I'm a professional compressionist, and ALL of our encoding machines are 8 core. We max them out all day, every day, and they are quite literally 2x faster than a single quad. Literally >90% scaling. No joke. On each machine we can encode 3 movies at once, at 40fps each.
Mostly the MB, video and sound. I've been reading the Apple support forums (mistake I think) and some of the "stuff" that is suggested there (mostly for trouble shooting OSX or hardware issues) boggles my mind.
I've never had to delete "preferences", "plists", repair "permissions", or reinstall my OS (XP home). Seems these are regular occurences for Mac users. Likely the reason there is such a well known procedure for booting off the opitcal drive or having the need for a complete system bootable back up. This stuff scares me off of Mac.
You sound a little confused. The MacPro is just a (very beefy) PC. Sure, it runs OSX, but why do so if you want to stick with windows? Use Boot Camp to natively install Vista x64, and get exactly what you want.
Any of these stated issues are a result of Mac OS X, and have little or nothing to do with the underlying hardware. You won't have them on Vista
To sum things up:
If you encode video, or do CAD / rendering - then get an 8 core. As far as 8 core systems go, the MacPro is unbeatable in price : performance, so it would be my firm recommendation.
If you don't, just get a vanilla single socket, quad-core system - or heck, even a fast dual core
~MiSfit