The best episode on the list is Bowling, by an absolute mile. I didn't vote for it though, because I wanted to vote for an episode where the focus was on Malcolm (or Reese's) relationship with a girl, whereas Bowling is more to do with the different approaches to parenting that Hal and Lois have. So i voted for Malcolm's Girlfriend, which is not a highly rated episode at all, but i've always loved it. I really like the way that Malcolm becomes obsessive and neurotic, and lets other areas of his life suffer, just for the sake of his relationship. It's a good observation on the way that teenagers (boys especially) react to the problems they encounter during their first tentative relations with members of the opposite sex. The way Malcolm is portrayed as being stuck between childhood and adolescence is very touching and thoughtful, even if it is played for laughs aswell.
I also think it has one of the all time best MITM mealtime scenes, which are often used in the show to move plots on and be funny at the same time. I just love the way that Malcolm's relationship is slowly uncovered by the family, and then the way that they react, particularly Lois. It's got great lines too, like Hal unable to comprehend Malcolm having a girlfriend because he's still "goofy looking". Also, on a somewhat unconnected note, Hal wielding a knife at the end had me in stitches.