So I'm relatively new to the monitoring of system heat, and I have been heavily monitoring my temperatures. My CPU gets up to about 48 C at its highest and I was worried that was too high. When researching the maximum CPU temperatures under load of my CPU (3960x), I found this thread saying that the maximum is 91 C under load. This seems way to high to be right, doesn't it?
No Those number are right. An overclocked chip will commonly run a lot hotter than 48C under load (91C might be the point where the cpu will throttle itself to prevent damage and is way too hot to run at for any length of time really). My i7-970 is clocked at 4.2 and will get up to 68C. I personally wont let my chip get over 70C as that is getting out of my comfort zone.
91C is too high for the CPU for long periods of time. Average working temps under heavy and full load are in the 60 to 70C range and they are absolutely fine. Although we all like to stay below 70 if possible.
For your rig, 48C is fine but I doubt it's under full load, try the IntelBurn test and keep your eye on the temps to see what is that max you reach.