Personally I like the third season the most.
It got the best characters, best story/plot, best Digimon partners, and the best music. Okay, "Butterfly" is the best Digimon opening ever but ?The Biggest Dreamer? is really, really catchy! X3~
And the second ending "Days~Aijou to Nichijou~" is one of the best anime endings ever! Ai Meada got such a lovely voice...
I also liked the card thing, card slash was it called I think. That was neat and the digimon battles got more interesting now when the Tamer also could participate and help their Digimon.
And I felt that the Tamers got a much stronger relationship with their Tamer than the other Digimon got with their partner?It happened a lot of things between Ruki and Renamon for example.(and Ruki and her mom too!)
The other characters where really interesting too.
Takato is the best goggle boy by the way. He is really sensitive unlike other ones....and his crush on Juri was really cute! :3~
Jrui was really interesting too, and who can forget the mysterious girl Alice?
And I really liked that this season was darker than the others and that Digimon actually could die.
You also got to know how the Digital World was created. And a lot of things happened and you got many answers and it had a good ending.
(by they way. I?m either talking about the Japanese or the German version. The English one is way too much destroyed so I can?t watch it anymore.X_x;;; )