The "two" important things, and a few lesser.
First, check to see what motherboard format your case was "designed" for. Most of your ATX mid + sized towers will hold and ATX or micro ATX mobo. Below that tends to get a bit more involved. In some cases where a tower was designed to hold multiple formats, the screw holes for the mobo will be marked as to that format. You mention having an aftermarket case, which is generally good for using a standard format. Be aware that some of the 'brand name' cases use screwball mobo formats.
Next, check the dimensions of your graphics card, cooler, and verify what PSU it's going to use. Generally you want to know the length of the graphics card. In the case of most ATX/Micro mobo it's height won't matter. Know the height of your cooler in reference to how it sits in the case. Is your PSU going to be in the way, etc.
Lastly, consider what drives you will be using and where/how they go in the old case. If swapping from 3.5 to 2.5 do you have the places to put them? Need adapters, etc. Its also a good idea to verify that the plugs on your PSU are what is needed by the newer mobo, GPU, and if really old your drives.