You will run into problems with fitment trying to use aftermarket standardized motherboards (Form factor, problems with I/O panels), power supplies (Form factor, size, in some cases proprietary motherboard connections) and graphics cards (Length and sometimes height).
You'd be much better to simply plan to replace the case as well as the motherboard and CPU. This probably means an entirely new build because you probably either have DDR2 memory or old, slow DDR3, that may not even work with newer boards due to differences in chip density between older DDR3 and more recent memory modules.
To avoid headaches and wasting money, I'd just plan for a new case, power supply, motherboard, cpu and memory. You can probably reuse your drives and...