Having built a few and bought a few

my only advice is that the main companies (Dell, Compaq, Gateway, etc.) have bits that are engineered and re-engineered to work together. Your lessor made systems might have quality components but if these components don't work well together then you've got problems. It's the total package that make these babies hum!
If you do decide to build a system don't forget to add the cost of software including the OS, as this adds up quickly.