A few things I learned as I built machines in the past (and/or fixed them):
1) Top notch Power Supply is a must. Something like a SeaSonic or other high quality brand name. There are really only two or three producers of Power Supplies, the rest get them from those sources and repackage them with their name (example - Corsair PS is made by SeaSonic). When looking for them, look for the 80plus symbol for high efficiency. If it is sized right for your system, those will be the quietest, most efficient PSU that can buy and that will save on electricity without sacrificing any performance. For my system (4 HDD - 2 SATA, 2IDE; ATI Radion x800 series GPU; Gigabyte MB; 4GB memory, 2 Optical Drives, 2 Magnetic Drives, & Creative Live Platinum Sound Card), I got a 500 Watt PSU which was a little high, but the next size down in the series I looked at was 300 Watt and that was a bit low. Given your specs, I would think a 500 - 700 Watt would be about the right size. Note, the design of many PSUs do not allow for power output anywhere near the rated output. Further research will find that many are actually 200 or 300 Watt Power Supplies using some sort of split rail mechanism and their marketing is saying each rail can carry the full wattage so it is 2 or 3 times the actual design spec. If you are an EE, you will certainly understand the details more than I, so I just suggest you do your homework there.
2) HDD - Like many here I find I have to side with Seagate on this one. I use the 7200.11 series and find them perfect for my needs. My problem with WD is that they always made my systems sound like they belong on a runway. In a datacenter that may not be bad, at home...
3) Sound - For people who don't know/care, I agree with integrated sound entirely. I will go that route from now on. When I bought my last card, onboard was just comming into it's own, so I got a card that had everything I liked. Now I don't use any of it's extra features and have a $200 card that I could have used onboard sound to achieve. Don't go for hype!
You sound like you will use it, however, and know exactly what you want so I won't push the issue any longer. The same can be said about video cards. Just make sure you know what you will actually use, and then work from there.
4) Memory - I agree that pretty much any brand name is good. I like Crucial, personally, but have used Corsair, Geil, OCZ, Kensington, and probably several others I can't think of now. The only one I ever had problems with was a single batch of Kensington and they responded promptly with good memory.
5) Monitors - Your biggest bane. Sorry, like others I can't really help. I have heard Samsung makes good ones, but I think most people just get what is available and stick with it for years and years.
6) Motherboard are a bit more mysterious for me. I find features I want then see what has them. I find Gigabyte and Tyan seem to be consistently good boards for me (Of course I don't overclock either). Though, I will admit that the last Tyan board that I have used is now over 10 years old. I tend to find Gigabyte boards as consistently the best bang for the buck (so the earlier statement doesn't surprise me a bit).
7) CPU is really a matter of taste and I tend to waffle back and forth on them. AMD are generally cheaper and comparible, but Intel does some things to keep them in the running. I use VMWare a lot, and AMD has been known to have some issues with virtualization so right now I am on more of an Intel kick. Give it another two years and I will be back in AMD's court.
The key I find is that it isn't the individual components that matter as much as the way they work together (assuming quality components are used of course). Look for key features, and make sure they all work together. Computers and components are constantly becoming more and more commodity items, so you should look at what FEATURES you use that differentiate them then work around those.
Enough of my two cents...
