The worse thing that could happen is that you could find out that parts wont fit and have to buy a new case. Just make sure that you set aside a little cash in case you need to.
Buy the motherboard and power supply that you want and check to see if it fits. If you buy a high end graphics card you may need to cut some metal to make it fit; this point is mote if the motherboard wont fit though.
Honestly I wouldn't even mess with it unless I wanted to do some kind of case mod. Anyway, if your case is ATX, then technically any new components should fit o.k.. If it's not, then you will not even be able to screw in the motherboard without modifying the case. Of course, if you are going to be using a tower cooler or a long GPU then it's always best to measure before hand.