Way to many amazing episodes to choose just one. So here is my list (not in order)
1. pilot- I always love pilots because they are where you look back when you are many episodes in
2. The Red Dress- The first time we see Lois and the boys at war
3. Lois vs. Evil- Malcolm's flirting is hilarious
4. Waterpark- There is so much change in character for this episode
5. Malcolm vs. Reese- We finally see thatFrancis treats his brothers worse than they treat Dewey
6. Evacuation- Malcolm's "first" attempt at becoming free of the the tyranic rule of Lois
7. Hal's Birthday- The relationship between Piama and Lois begins
8. Family Reunion- The last 5 minutes are just great and say a lot about the relationships in the family
9. Stupid Girl- Malcolm is just hilarious
10. Fowards Backwards- May be my favorite because of the filming perfection
11. Malcolm Holds His Tongue- His thoughts and the reactions to his silence are great
12. Vegas- The rabbit and Lois are the best to watch
13. Thanksgiving- Malcolm drunk?

14. Ida's Boyfriend- was not expecting the end
15. Billboard- Reese's dream
16. Blackout- amazing filming
17. Mono- Lois and Malcolm are unreal
18. (out of order) Halloween- The old man gets his revenge
19. A.A.- My favorite episode of Francis
20. Graduation- I can't say this is a favorite, maybe my least favorite just because it means the end. However, it ended the series by bringing it right back to the start in many ways.
Wow, I kept it down to 20, I'm sadly proud of myself

Even considering I havent yet seen all of the episodes