Instead of dropping money into a prebuilt, you might as well get an entry level system(if it's for gaming). The issues accompanied with a prebuilt is that the front panel connectors aren't labelled so adding a new board(although labelled on the board side), isn't labelled on the wires.
How much are you looking to spend, where are you located and why are you upgrading?
I've been upgrading this PC for years. I've changed it to a AMD Athlon 64 Dual Core because I found out that they are faster it you're not doing a lot of multitasking. About the only thing original is the Motherboard which is stopping me from upgrading any more. I'm around Detroit. I was hoping to keep it below about $300.