it really depends on what you have running.. there is no one solution for every setup. the comp im using now runs fine in its case with a low cool air intake and an exhaust at top. it also runs fine with it outside the case. when i tested this i used it alot and periodicly shut the pc down and toutched the heatsinks (always make sure to discharge static before toutching anything in your pc!!) , power supply, and some other known hot spots. there was no difference with the case on or off, so i put it on just to keep dust off the components...
on the other hand, alot of new stuff runs hotter and will break down if you let it get too hot. one option which i am gonna use when i upgrade my pc, is to put a thermomter inside so i can know if the heat is really getting bad. leaving it in the case is safer but its no guarantee. you should still check on it and if its getting too hot, try taking the components out and make sure there is plenty of ventilation and air blowing across the area, especially the cpu and vid card.
also.. your setup might be fine until summer hits. check it alot to make sure its working alright, especially on the hottest days and then you wont have to worry about it anymore.