I voted for season 2 (If I had known that you could vote for more than one season I would have voted for season 3 and 4, too
). Though I think that each season has its great episodes and moments, I think that season 2 has most of the classic episodes. Season 1 was great, too, but it´s mainly focused on Malcolm and the other characters don´t have many own storylines. So this is what I personally like more about season 2. Season 3 is pretty good either. It was a little different from the 1st and 2nd season because you could really see how the kids had grown and their storylines became more adult, but it was a great season. I have to agree with the previous poster that season 4 was good, but the Francis plots were pretty weak. That´s actually also the only thing I didn´t like about that season.
Season 5 is my least favourite. I can´t explain why, but I think it had some of the "worst" (though they weren´t really bad) episodes. I think you could also see the way many of the characters had changed. Malcolm wasn´t that important to the show anymore and Dewey turned from the little weirdo he used to be into a smart and sarcastic kid. He also suddenly got along with Reese pretty well. I don´t think that all these changes were bad, but it was different from the original concept of the show, I think.
Season 6 seems pretty good to me so far. Standee, Malcolm´s car and Busey´s runaway weren´t the greatest episodes, but I really liked Pearl harbour, Hal sleepwalks and Reese comes home.
So I hope they´ll renew for a 7th season.