I am seeing a lot of negative talk about third-party software to control fans:
Istat menu 5 is good.
It conforms to apple's SMC; this means that it will never allow the fans to go slower than what SMC is asking, thus your computer will be safe using this software.
In contrast I have a Macbook Pro fan controller for bootcamping Windows 7 called MacFanx64.exe (64 bit) that requires you to understand command prompt.
It's nothing difficult, you just need to make sure that you enter parameters properly.
The only way I see one of these damaging any hardware components would be if you accidently told the fan to spin faster than the max speed.
I would agree that for OS X you aren't going to really need this because the engineering on the SMC isn't terrible, but if you happen to have SMC screw up like it sounds like you had, there's no way to know it unless you feel it getting really hot like that which I'm sure isn't great for your MBP.
Therefore having a monitor system is helpful because you can see the temperatures constantly.
Now for Windows 7 bootcamp it's a whole different story.
There is something wrong with the drivers that control SMC for bootcamp because the computer will get hot fast even in idle.
I was marking temperatures around 60-70 C just in idle - the fans still stay at 2000 rpm.
If someone finds something better than MacFan for Windows 7 bootcamp let me know.
Moral of the story, if you pick a good third-party application you're not going to harm your computer.
Think of it like a second line of defense.
Last but not least, if you're still having this problem do an SMC reset.
Apple has instructions on how to do it, just note that you need to pay attention to whether your MBP has a removable battery or not when doing SMC reset.
Cheers