The only thing that I know is that Cypionate is probably a tad slower releasing and has a little longer active life. This is due to it having an 8 ester carbon chain as opposed to 7 with Enanthate. That is one difference, the other is that Testosterone Enanthate is a little more potent per mg than Cypionate, just because of the fact that it is 1 atom lighter. The difference in strength is very small (we are talking a few milligrams).
All in all they are very similar with Cypionate being slightly more expensive usually.