Wow, how did I not see this thread sooner?
Okay, in order from most favorite to least favorite . . .
#33: I love the character development here for Tobias, and it was a very sad and emotional book, and I love that. I like any book that can bring emotion out of me, and this one does it for me in spades.
HBC: Another emotional book. You know from the beginning that the whole war they're fighting is pointless and that Dak is doomed, but you can't help but root for him anyway. Plus, this book is the source of some of the best quotes in the entire series, in my opinion.
The Ellimist Chronicles: Holy-shiz wow. Very good story, only slightly hurt by the fact that some of it leaves readers a bit confused (if it weren't for the constant obstacles to comprehension, it would have trumped HBC easily), and very emotional. Still, I think that writing it with little description was an artistic choice, so I respect it. It serves to sort of alienate us from the Ellimist, just as he is alienated from everyone else. Still, it does make it a bit harder to read than HBC or #33.
#41: A very good book, once I learned to stop trying to make sense of it. I've finally decided that it has to be nothing more than a dream sequence, but it is still incredibly meaningful and drenched in metaphors for Jake's eternal struggles. The fact that Jake's mind is even capable of inventing such a twisted scenario tells you more about his character than most of his other books. I also liked the ambiguous ending, where all they tell you is that Jake made the choice that 'should have been obvious.'
Visser: I would have thought it impossible, up to that point, to sympathize with Visser One. But this book manages to pull that off. At the beginning of the book, you're like, "Yeah! Die!" And by the end, you're like, "NOOOO!" I was actually heavily disappointed when Visser One actually does die in #45. All she ever did wrong was to love . . .
#45: A very good book, despite V1's death. This marked one of the big turning points of the series, where everything starts going to hell. Marco is forced to tell his father who he really is, which is a really charged scene, and kind of sad how hard it seems to be for his father to accept the new reality.
#49: Obviously, another huge turning point. I think it's extremely sad to watch Tobias find his mother, and then hardly know what to do about her. The idea of family and love being such a foreign concept to him is heartbreaking. Also, of course, as has been mentioned by other people, this is the book where the Animorphs have to rescue their families and say goodbye to their lives as normal kids forever.
#13: Hehe, I like Tobias books. Can you tell? This one is another character-revealing book, and I think it's deeply meaningful how he got his powers back instead of becoming human. Whether he knew it or not, the Ellimist was only granting his one deepest desire. To fight. Not to become human. Because he never wanted to be human in the first place.
#1: Yes, this book was more riddled with KASUs than any other, but let's face it: this was the book that hooked us all. It showed the struggle of five until-that-point normal kids who had suddenly been thrust into a war. The fear and uncertainty of it all was completely new to them, and I think KA captured their reactions very well. This was what set the stage for the Animorphs as potentially real kids, not just characters in a story. How they reacted was exactly how any real kid would react. Being scared out of their minds, yet still they stayed in the construction site to watch Elfangor's ship land. And let's not forget the shock and horror of seeing the Yeerk Pool for the very first time.
TAC: Just generally a good story. Elfangor is a great character, and watching his mistakes and consequences feels very real, like you're there with him. Also, it's ironic how a few of the scenes from this book are re-played later in the series. Elfangor's decision not to harm innocent Yeerks, for example. Jake is faced with the same choice in the final battle, and makes the opposite choice. A parallel that seems to show that Elfangor is actually less battle-hardened and ruthless than Jake. Not to mention that Elfangor rammed a Blade Ship and survived . . .