First, make sure that you have intake and exhaust fans running (I ran one the wrong direction once and had some issues). Next, if you are using a stock CPU cooler, toss it. Buy something like a Zalman that has good specs. Also, thermal compound is a must.
the stock cooler should have come with a cheap wad of it (the gummy grey stuff on the bottom of the heatsink). If you have a local computer shop, they should have thermal grease. If not, newegg and tigerdirect have it. You only need a dab, but it makes a huge difference in temperature. The problem with thermal grease, including the stock stuff, is that if you move the heatsink, you have to scrape it off and put on more. If you have moved the heatsink, that is most likely your problem.