Sounds good. Let's see...
If it's a work machine (not strictly gaming) and you're the kind of person that keeps a PC for several years with only an occasional upgrade, then you should get a quad CPU.
I think the Q6600 would be best for you. If you have a very good budget, then Q9550.
Video card: HD 4850 is about $160, handles Counterstrike without any problems, and has HD support. Best bang for the buck these days. It can run a bit hot, but the NZXT Tempest can handle that easily. BTW, the RC-690 case is also very good at cooling, and cheaper. $77.24 with free shipping here:
http://www.buy.com/prod/cooler-master-690-without-power-supply/q/loc/101/206177908.html
You definitely don't need a multi-GPU setup (i.e. SLI or Crossfire) for Counterstrike. That is, a MB with a single PCI-E x16 slot should be enough.
However, if it's a work machine you might want to use 3 or 4 monitors at some point. With 22" LCDs at $200 and falling, I think it's likely. Since a typical video card supports only two monitors, you'd need two video cards. The card used for monitors 3 and 4 can be a $30 HD 3450, it doesn't have to be a gaming card. I suggest you get a GA-EP45-DS3R if you don't trust Asus. You don't have to buy a second video card yet, of course, only when you buy the 3rd monitor (if ever).
No worries about IDE ports. Almost every modern MB comes with an IDE header that allows two IDE devices.
RAM/Windows - it really depends on what you're doing with the computer. Counterstrike would be OK with XP 32-bit and 2 GB of DDR2-800. Crysis would look nicer with Vista 64-bit/2x2GB DDR2-800. If you do certain types of work you may even want 4*2GB RAM. Either way, since you consider yourself a noob, I'll assume you won't overclock and that means DDR2-800 is fine, you don't need more expensive DDR2-1066 or more. If in doubt, get 2x2GB and see in Task Manager over the first month. If you are using over 3GB often, add 4 more.
PSU: if you go with Q6600/HD 4850 then something around 500W would already be acceptable. It's best to give yourself some upgrade room, so I'd pick a 550VX ($78) or even 650TX ($90).
http://www.newegg.com/Product/Product.aspx?Item=N82E16817139005&Tpk=650TX
http://www.newegg.com/Product/Product.aspx?Item=N82E16817139004&Tpk=550vx