As far as the manufacturer goes, I recommend going with a bigger name company such as Gateway, Compaq/HP, Apple, or Dell.  Check the warranty on the computer...most come with a one year limited warranty.  Milwaukee PC is another excellent place to have a computer built for you.  Gateway has "Country Stores" on Brown Deer Road and also on Bluemound.  Their Country Stores offer an excellent opportunity to try before you buy.  If you already have an adequate monitor, keyboard, mouse and printer, you can save a substantial amount of cash by just buying the tower. 

Even if you buy a new computer, consider adding memory (RAM) to your existing PC so you can have more than one PC in the house.  Also, consider creating a small home network to share printers and your high speed connection to the internet amongst several computers in your house--this is great if you have several kids who are competing for home computer time.  A mixture of a wireless network with a few network cable drops usually provides ample network coverage for a house.

A word on software:  This can be the most expensive part of buying your new computer.  If you buy Microsoft Office (this usually includes Word and Excel--for additional money, you can add programs such as Power Point and Publisher) make sure you get the educational discount.  Without the discount, office is EXTREMELY expensive.  When you are at a retailer, just show some type of proof that your son or daughter is a student.  Middle School software list

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