I would be hard pressed to name a favorite episode... but the ones that come to mind:
Waterpark - I think every trademark MITM element was in play here and in perfect balance. The Malcolm/Reese rivalry, the Hal/Lois relationship, Dewey-ness
, and strange elements like the hamster ball! And with the abrupt end to the babysitter (Bea Arthur) punctuating that dance to Abba's "Fernando" - wow, everything was going here!
Smunday - Lois rising from the bed like a vampire, clutching Francis' letter!!!
Reese Drives - Great lines in this episode - the police bullhorn interpretation of Lois' demands - and Reese's reaction ("That's not my mother!") and of course, the Dewey/Reese wars - ("Give them a reason! Give them a reason!")
Ida's Boyfriend - Grandma be drugging the man from China! And the Dewey/Reese wars at their best when Dewey wishes Reese away and grabs the dumpling.
Graduation - Lois' speech at the end brought tears to my eyes. I couldn't stop sobbing, especially when she talked about why Malcolm should be a great president. It was a perfect bookend to the premiere episode.
Over all the seasons, I think Reese's character had problems in Season 6 and 7. It was one thing to make him a bully/thug, then a budding chef, but then when the writers emphasized his dumbness, I think that didn't ring true to me.
Malcolm, Dewey, Francis, Hal and Lois - definitely loved the characters' evolution over the years.
And great secondary characters like Grandma Ida, Craig, Stevie, Abe and Kittie were great comic foils.
I especially loved the early seasons where Abe and Kittie were the most overprotective parents ever!
So much great writing I miss! That DVD set is sorely needed!