The way to go is to really build your own. It sounds a lot more complex than it is.
If you already have a case (if you are upgrading) you don't have to worry about that much.
First think about the CPU you want. That's the first thing you consider. You decide what kind of processor, what style chip (i.e. a LGA775 or a Socket A) and what speed. Just look at speeds, and then find out what the socket-type is for that chip.
Second find a motherboard in that socket-type. The motherboard has to be able to hold the CPU, which is why I said think of the CPU first. I use newegg personally, but you can use any online website to find out the specs on motherboards. Once you find a selection in the socket-type you need, there are other considerations -- find one you like.
These are no-brainers. If you want to be able to plug in several PCI cards, you need to find one with 3 to 5 PCI slots. If you want to use your PCIe 3d card you need to find a PCIe motherboard. Basically this is the "what do I have, or want, and how many slots will I need to get there?" step. You don't need to know anything special at this point, you're just adding features in your head.
Once you have that narrowed down, you need to take note of what kind of RAM the motherboard supports. There are 2 major types right now, DDR and DDR2. These are not compatible. You can use one or the other. DDR is PC3200 and the like. DDR2 is found more often on AMD motherboards (just a personal observation). Some mobos have slots for both types, but can only operate with one type or the other installed. You need to buy RAM for the mobo based on the type of RAM it supports. If it's neither of these types keep looking -- you've found a mobo that supports and outdated/old/obsolete/obscure type of RAM and it will be expensive as hell to purchase any.
SIDE NOTE: Read the motherboard specs. Find out how much RAM capacity (total) the mobo can support. If it's got 2 slots it might support only 2GB total. That hinders you a few years from now when you need to upgrade. You can get "value" RAM as long as its by a decent company. When in doubt, your mobo should have a vendor list of all supported RAM types.
So that's the CPU/Mobo/RAM. You've already built the PC there! Basically ...
Now just "accessories". One thing to consider is a new PSU. Newer chips and mobos require stronger PSU units. Certain mobos have voltage requirements and state as much. If your current PSU doesn't fit the bill you need a new one. Just look at the total W supplied, and the volts on the 12v rail etc etc. Compare to what the mobo needs (and/or your 3D card if it needs special requirements). Again, basic math ("How many Watts do I need? Of that how many Volts do I need to power the motherboard? Okay last addition, how many special connectors do I need for my PCIe card")
Then plug your vid card in. Plug your sound (if you have a PCI sound card, most mobos have onboard sound now), plug in your NIC (if applicable), plug in anything else, HD, floppy, CD-ROM, etc, just like you're swapping parts in or out, only you're doing it to a new mobo.
Stick the Windows disc in the drive and boot her up! Reinstalling windows is the best thing to do with a new motherboard. Once windows is done installing, you may need to pop in the mobo CD-rom with drivers, and/or CD-ROMs from your other cards (vid, sound, NIC, etc).
You've just built your own PC!
The tricky part is really just CPU/mobo/RAM/ and-or PSU.
