Yes, there's a difference between GDDR3 (graphics cards) and DDR3 (regular RAM), GDDR5 is not far away last I heard.
Anyways, the problem with "cheap" DDR3 memory is that they have high latencies. It's not only the MHz that tells you how good a RAM is. A high clock can make up for the difference but you must be aware that the latencies eats up some of the speed increase, and are you willing to pay for what's left? Prices will drop as DDR3 becomes standard, early adopters beware.
I'm not into motherboards, just make sure the one you got supports DDR3. Also high speeds don't make up for volume. When you run out of RAM your hard drive will do the work for you and that's always very slow.
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