The difference, in essence, is speed and accuracy.
With one pass encodes, the encoder will move through the material just once examining the motion and estimating the best encode rate for each particular section, and for the settings you have put in place. It estimates, encodes and moves on.
With two pass encoding, the first pass is used to analyse the motion and the second is the encoding - this is why the second pass takes so much longer. It is largely more accurate as it establishes the best encode for each section and then applies that on the second pass.
Cinemacraft does multi-pass encoding, with each sweep refining the analysis made on the previous pass. Such a technique realy helps get the very best from the footage and this is why Cinemacraft is so highly thought of.
However, the draw back is the time it takes... 2 pass takes longer than one pass, although the quality you get for the same (or similar) resulting file size, is better.