While detailed recommendations would depend on the types of things you want
to do with the computer, I highly recommend the new Intel Core 2 duo
processors over the current crop of AMD as well as any of the older Intel
models. The cost savings on electricity to run the system over 3-5 years
with the Core 2 offerings is easily overlooked and should be well worth any
premium you might have to pay to get one.
Other generic recommendations IMHO:
RAM - Get as much as is reasonable in as few DIMMs as possible, with as fast
of a bus speed as affordable, 2x512 (1GB) 533mhz minimum, 2x1gb (2GB) 800mhz
would be better. Make sure the motherboard supports at least 4gb of RAM. 8gb
would be better.
Graphics - If you want Aero Glass capability, be sure to verify that your
graphics will support it. Most built-in graphics won't.
Hard Drive - Get as much as the manufacturer offers at a "reasonable" cost
for your boot drive. Remember that upgrading this first drive is much more
involved and so make it a good one. I would consider 160gb 7200rpm SATA-II
the minimum these days. I know it may seem like a lot but as soon as you
start using Media Center or any Video work, you'll eat it up quick. Also,
make sure that the system supports at least 2 drives. Those micro cases with
room for only 1 drive are incredibly frustrating to try to upgrade.
Optical Media - Don't even bother with a CD-ROM. At a minimum, a full
double-layer, +-R/RW shouldn't cost more than about $80 now. Anything less
will be obsolete before the rest of the system.
Floppy - Don't bother. If they offer a memory card reader instead or more
front USB or Firewire - take it instead.
Network - at least 100mbit built-in is probably the minimum all around. Get
Gigabit if you can and it's not too much more. Don't fall for built-in
wireless, A, B, and G are all too slow these days. 802.11N is the future but
the standards have been slow to finalize.
TPM - somewhat obscure but this is the enabling technology for the future of
encryption on the desktop. You may not be able to find anyone who can tell
you if their systems have it or not though.
I'm sure that there are other areas that I haven't addressed and some will
certainly disagree with some of my recommendations.
By the way, I highly recommend building your own too. Even though it will
almost certainly cost more and take longer, you will have an intimate
knowledge of your system that can only be understood by other home-builders.
Good luck.