what fan doesnt even run? the cpu fan or a case fan? that sounds odd to me...but as far as leaving the side panel off you just have to be careful and keep it in a place that something wont be able to get inside the case....kids touching crap...something falling off your desk etc....also you gotta be more mindful with dust build up in the system so you gotta clean it out a little more often...other than that there is not too much risk running the pc with the side panel off if you take the necessary precautions...I wouldnt do this with my pc's personally I would just add more fans to the case or cut a vent hole in it or something...
There's a small suction fan at the top/back with the power supply, it doesn't run when I have the case open, I guess because the system is cool enough.
On closer inspection I found that the noisemaker was actually the video card fan. It was blowing hot air out of it's exhaust slots that was too hot for my finger when I pressed it against the exhaust. This exhaust was right against the case cover.
I'm going to cut a vent hole, good idea.
I was wondering though, is there some suction cooling process that makes the air rush faster when the case is closed thereby requiring the cover to stay on?