1) How to maintain low CPU temperature ?.
2) What are the factors that cause high CPU Temperature ?
3) what are the chances of damaging my motherboard due to excessive heat released from processor, hard-drive , additional chip-sets. etc
Apply proper cooling in your computer. Also, make sure your CPU runs on an "on demand" or "powersave" mode. This will put your CPU speed setting to as low as possible. (On demand puts it as high as your computer "demands".) Also, disable CPU eating background services and processes that will cause your CPU to run at full capacity.
When more is asked of your CPU, the clock of the CPU is turned up to allow more calculations per second to be made. A higher frequency will also mean more electricity will pass through the circuits, causing more heating of the CPU. So the more processes demand CPU time, the hotter the CPU will be.
Next to CPU usage, also the cooling is a factor that can cause a higher or lower CPU temperature. The better the cooling used, the lower the CPU's temperature will be at high performance.
Newer motherboards have lots of fail saves that also monitor CPU temperature. Once it gets too high, the motherboard will disable the CPU and shut down automatically. So the chances are quite slim that damage will be done to other components due to excessive heating.
This is not the case when you're running the CPU whilst being cooled and suddenly remove the cooling whilst in operation. This will most likely result in a nice hole in the circuit board of your motherboard. Not so desirable. Moral: Don't turn on a computer without CPU cooling.
Nice addition from Chris S's comment:
This is true, that's why most BIOSes have the fail saves set so that it's within reasonable parameters. Changing these temperature values would not be smart if you're concerned about damage due to heating of the CPU! ;)
Here is a good cooling guide from Toms Hardware for the 1156 Intel processor, but the concepts work for all CPU's.
There's another article stating whether using the stock fan is good enough
And finally there's an article comparing simple water cooling versus air cooling