The first one featured Shinji, Asuka and Rei with the Eva 01 as their background.  These quickly sold-out, so a second printing with the same cover came out.  The only difference is that if you look closely at the card wrapper, it will say that it is the second printing.  They cost cheaper too.

The third series had Rei as the cover.  These presented the Evangelion trading cards in a revised lay-out with additional cards, characters, etc. etc. that weren't part of the first two.  A second part for the third series came out with Rei and Pen-Pen as the cover.

The most expensive card line was from the movie.  These cards entitled from the two Evangelion movies were considered in the 'wide card format' meaning they were taller than the average trading card.  These are still available until today at some comic stores.