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Your heat sink fins are likely clogged with dust.
My 2008 MB Pro just recently died and the Genius Bar told me my motherboard was toast. I was used to it getting pretty hot and figured a solder joint had cracked. I had nothing to lose so I took the whole thing apart and reflowed the motherboard in the oven at 400F for about 8 min. Its working fine now but I made sure I thoroughly cleaned the inside including the heat sink fins, which were nearly completely clogged with really sticky grime and dust. It is running much cooler now.
To answer your other question, the majority of the heat is created by a few chips on the motherboard which are connected with thermal grease to your heat sink. The heat sink extends to either side with cooling fins that your fans blow air through. If these are clogged, you are not expelling as much heat.
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