1) If you're going to spend $160 on a quad-core Phenom, then you might as well plunk down the extra $40 to get an i5-750. It's a much faster CPU thanks to the turbo mode that does an on-the-fly low-level overclock when less than four cores are being used, and it's a stellar overclocker as well. That said, you won't see much drop in performance if you decide to go with a much cheaper Athlon II X3 435 or X4 630 instead.
The cheapest motherboard which supports the same features is $40 more expensive, so for a marginal upgrade he would have to pay 1/3rd more overall, not counting the MIR.
2) Not a knock against your build, obviously, but you definitely don't need more than 4 GB RAM unless you're running some sort of really RAM-intensive apps on a regular basis. If you have to ask whether you need more than 4, then you probably don't.
Its simply tidier to use 2x2GB and cheaper to support 4GB. Also it gives the option of upgrading even if its never taken up.
3) The Sonata 3 is a decent case with an equally decent bundled PSU, but if your budget permits it I'd advise going with a 550W Corsair or SeaSonic, an Antec P180 Mini (the best price:performance case on the market right now), and a Micro-ATX mobo.
Unfortunately budget doesn't permit. 
4) The SSD is a nice idea that will give you faster boot/load times on games and productivity apps, but I'd recommend going with an
80 GB Intel X25-M instead. There's nothing wrong with the OCZ, but the X25-M is slightly faster, can hold 20 GB more stuff, and is only slightly more expensive. But again, only fit this in if you can afford it.
That could be worthwhile, they both score very highly on the AMD SSD bench. Its definately swingable if the OS is downgraded to Windows 7 Home premium and the extra 20GB of space yields more flexibility.
5) The biggest factor in HDD speed is something that isn't usually advertised on Newegg or elsewhere: The number of platters. One or two high-density platters means faster seek and write times, and the 750 GB Caviar Black has three 250GB platters - not exactly ideal. Look for a Caviar Blue or Black (or Spinpoint F3, if you can find them) that's either 500 GB or 1 TB, whatever your budget and needs permit, and Google a couple of reviews to check how many platters it has before buying.
Good point, I forgot about that. A WD Caviar Blue 500GB might be a good idea for $55 and it saves $15 which along with a downgrade to the Windows will allow the larger 80GB SSD. http://www.newegg.com/Product/Product.aspx?Item=N82E16822136073&cm_re=caviar-_-22-136-073-_-Product
Can anyone care to explain why the i5-750 is better than a Phenom II X4 965 when Passmark.com rates the Phenom higher on its user benchmarks? Curious to understand why...
I don't think its worth the price relative to the phenoms, see first quote for the $80-90 price differential.