Well, apart from the physical differences between the two; the Cat5e standard is rated for frequencies of 100Mhz, whereas Cat6 is rated at 250Mhz. What does this mean to you? It means that over long distance runs, you will be able to maintain a higher data rate with Cat6 than with Cat5e. However, the difference will more noticeable with 1000BASE-T Ethernet than it will be with 100BASE-TX.
If you would like more information on the two, wikipedia is a good place to start: Cat5eCat6
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