The difference is the bus speed 667MHz vs 800MHz. If you'll notice the difference, i don't know for sure. What is certain, is that the 6400 will transmit data faster than the 5400.
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I use 2GB dual channel PC5400 in my rig and it does the job beautifully. 6400 is faster but like tijo said you might not notice the difference. You'd prolly only notice the difference if you do alot of high performance computing where you grind through alot of memory and speed becomes highly important.
But if you're just playing games etc. 5400 will do the job just fine.