I'm surprised, no one's mentioned my three favorites!
1. #30 The Reunion - I didn't "get" this book as a kid, but as an adult I understand it. The way the writer handles Marco's desperate fall into ruthlessness is pitch perfect, and the insomnia chapter of him explaining his actions to hypothetical people is one of my favorite chapters in the whole series. "This is how I destroyed you, this is how I saved you" and "The Marco dude? He was cold" are some of my favorite bits. There's also some interesting material with Jake, some elaboration on Marco and Rachel's uneasy camaraderie, and it cements Marco as quite possibly the most ambitious tactician in the group.
2. Visser - Finally, Visser One as the main antagonist! I thought this point of view from Edriss was fascinating, and more detail on the Council of Thirteen is always welcome. The idea of Yeerks going human, or becoming addicted to humans, is fantastic and compelling. There's also some great writing, from the line about controlling Madra at the end to the believable reversal of charges Edriss pulls on Esplin. "I made Jenny Lines breathe" is a chilling scene as well.
3. #15 The Escape - Probably one of the most solid of the books in the teens, which was already pretty golden when you consider it includes #13, 15, 16, 18, and 19. The parrots scene is an example of the silly opening plot adventures done correctly and humorously, the shark in the pool scene casts Marco's character in a very interesting light, and the finale to the book is sufficiently emotionally packed. Also, both "acquiring the morph" scenes are very fun.
4. #19 The Departure - Needed to happen. This book was a game-changer, in that it elevated the Animorphs from a fun kids' series to a thoughtful kids' series with relative morality. I only wish we'd seen more of Aftran, since she's fantastic here. I also really related to Cassie's doubts and moral struggles, and felt for her when she made bad decisions, even if they eventually worked out.
5. #3 The Encounter - The introduction to Tobias is thoughtful and beautifully-written. I'm surprised at how dark it is, even for a kid's book, as to have a suicide attempt halfway through. Personally, I think this is Tobias' existential crisis at its best.
6. #22 The Solution
7. #26 The Attack
8. #33 The Illusion
9. #10 The Android
10. #52 The Sacrifice
Honorable mentions to #5, 8, 16, 23, 31, 35, 49, 50, 53 and 54.