Find a local computer store (not a big box retailer), and then go to him/her with the specs you want. They will build what you want the way you want it.
Here is what I would look for:
Case: I would look for at least one 120mm outtake, and preferably, another 120mm intake. These will keep the insides cooler, and are quieter (generally) than smaller 80mm and 92mm fans. I like the Antec Sonata III. I also like the Sonata II, but the included power supply might be a little underpowered.
Power supply: 500 watt minimum. Preferably, unless buying an Antec case, not one that comes with the case. They tend to be less reliable. The Sonata II has a 450 watt power supply, which should, if you do not envision adding components, suffice for the system.
CPU: I’m partial to the Intel Core 2 Duo E8400 Wolfdale 3.0GHz 6MB L2 Cache. Lower power requirements means your CPU fan has to work less hard, which means quieter computer. And it is a little cheaper than Kinthalis’ recommendation.
Motherboard: I would opt for a motherboard based on Intel’s P35 chip, versus one based on nVidia’s 780i. Generally speaking, unless you go with the best, most expensive videocards, SLI is overrated versus just upgrading your current videocard.
RAM: 2 gigs. Should have a heat spreader.
Graphics: NVidia GeForce 8800GT (not GTS), 512mb. Again, a cheaper option. Don’t skimp here if you want to play Spore and BioShock. Stay away from any videocard that has 320 or 640 mb memory. That is old stock.
Hard Drive: At least 320 Gb. 500 Gb would be better.
OS: Vista Home Premium will allow you to enjoy your games in DirectX 10 goodness. XP Pro will be (slightly) less of a headache.
20" LCD monitor.
Let your local shop price this for you - itemized would be better.
Don’t forget the DVD/CD burner.
(In case you missed one of my themes, I like quiet PCs)