There are two key differences:

1.Signal to noise ratio
2.Bandwidth used to test the cable

The signal to noise ratio is the most important. Cat 6 is less "noisy" by twelve times than Cat 5e. Your data packets are lost or changed along the way when your computer transmits data across your network. These packets must be resent by the system. The better the signal to noise ratio is on your network, the fewer times this will happen.

As computer networks get faster, the signal to noise ratio gets to be more important. If the network is getting backed up in packets that need to be resent faster than it can resend them, the network may sometime not work or slow to a crawl with the backlog. Using cable and components that have better signal to noise ratios, like the ones rated to Cat 6, can help to keep this problem from happening.

As far as the testing bandwidth goes, the official Cat 5e customary calls for testing across a bandwidth of 100 MHz. The Cat 6 customary calls for testing across a bandwidth of 250 MHz. Most computers and networking equipment only transmit across a frequency span of 100 MHz. (Actual utilization of greater bandwidth may start to be more common.)

In all actuality, this particular statistic isn't really that important. Several cable companies hype the high bandwidth of their cable. Some even test as high as 700 MHz. It sounds wonderful for marketing, but it really is that the MHz rating is different than speed. All cable rated Cat 5e or Cat6 is capable of Gigabit Ethernet. The MHz rating is just the frequency span used to test the cable.