First you have to decide on the type of build in mind when preparing for the type of system to be assembled. If this will be for gaming or simply high performance then that will see a higher total using a fast cpu, high end video card, and a good amount of memory. The Acer prebuilds are a lower quality premanufactured system.
For gaming most will point out one particular Core 2 Duo or quad core model they favor for things like ocing. For a basic web browsing email checker you can save a bundle cash wise simply deciding on how large a drive will be needed along with seeing 1gb to 2gb for XP and 2gb seems right for Vista.
The usually accepted as top makes of boards are now seen as Asus, Gigabyte, MSI, and EVGA. You start with a board first that offers the features as well as socket type for then choosing which cpu will meet the needs there. What the board supports for memory as well as the cpu is still first however.
For a basic AM2 board at this time for 2gb of DDR2 800 memory and a dual core AMD cpu the Asus M2N-E works for $99.99 down from the $135 seen last August.
http://www.newegg.com/Product/Product.aspx?Item=N82E16813131022
The AM2 6000+ X2 was seen for $229.99 then without the slightly faster 6400+ X2 model seen at the time
now for $169.99.
http://www.newegg.com/Product/Product.aspx?Item=N82E16819103228
2gb of Kingston memory was seen for $88 then is now $44 at
http://www.newegg.com/Product/Product.aspx?Item=N82E16820134488
$80 for a WD 320gb sata drive.
http://www.newegg.com/Product/Product.aspx?Item=N82E16822136074
Sub total before S&H = $394 + or - a few cents
Video and even sound card will depend on need. ATI is known for image quality while NVidia cards are favored for gaming. Then add that to the case and power supply. The links here are only a rough idea and can be changed at any point to give you an idea. The make and model board would be different if deciding on an Intel rather then AMD cpu.