Forget about AGP, its dead. Forget PCI as you will probably only install 1 or 2 cards in the computer( thinking sound and TV cards). Ethernet is standard on all newer motherboards. Yes the 8800 Nvidia graphics cards are still tops but unless your a gamer you really don't need it. PCI 2.0 is just a standard. What your really looking at is PCI_E which is the new standard for graphics cards. Most new MB's have at least 1 or 2 PCI-E slots. What you do need to look for in PCI-E is a 16X slot ( maybe 2 if you want SLI) for the best graphics cards, if you think you need one. I usually look for on-board graphics like the 6100 or 7100 serices chipsets on many of the newer motherboards. They do just fine for most computing needs.
Ram needs is simple in that you really don't need more than 2 gigs of memory unless you want to game. If your gaming then you will build a whole different computer from the ground up just for gaming with 64 bit MB, OS, and 4 gigs of memory and usually SLI.
What i like about the new system is they run pretty cool. A basic system of a better CPU heatsink, and a 120 MM good power supply, and maybe just a intake fan to keep things moving thru the case is really all you need. Check out the zerotherm, zalman, and thermotake CPU coolers at newegg. Also look at the Power supplys there. There are reviews on everything at Newegg that you should read. I like Power PC and cooling, Silverstone, and enermax power supplys.
Cases i like to get whatever is handy as most go out the door within a month. Heres a good place to look at different types.http://www.directron...-atx-cases.html
So theres a start for you. Just remember that a couple of years from now you will probably want a new computer. So i limit myself to Less than $800 on any computer i build for myself. I usually get by with around $500-600 for my computers.
I have a Q6600 quad core/XFX 610i MB comp and also have a dual core 2.2 Intel 965 MB comp and i really can't notice any difference in the speeds on any programs i use. My quad core seldom uses more than one of the cores for most of the programs i use. I have a widget on the desktop that shows core usage so i watch it quite a bit. SO, i would conclude that a Core 2 Duo 3.0 would probably be better for most applications on any computer.
A Wolfdale E8400 3.0 CPU costs $190. Its a 1333 FSB, 65 watt processor. The Q6600 i have is a 95watt 1066 FSB, so it runs hotter and has a slower bus speed. The Q6600 is the same priced as the E8400 so you can pick what you need. If i had to do it over i would have picked the wolfdale 3.0. I'm still running a old pentium 4 - 3.0 computer i built 3 years ago every day so i would not worry about longevity. I do like running intel motherboards, but this time i picked a tiger direct kit that had the XFX motherboard. I have not had any problems to date on this computer. I also like the Gigabyte motherboards, but these EVGA, XFX, and other company's have much better prices for what you get. I like to keep as much as possible to on-board motherboards because there is usually less problems that way. I really like to throw the computers together, fire them up, install a OS and ship them out the door. That is why i tend to be conservative in my builds. I don't like them coming back with problems( other than the one's caused by customer's).