I went to visit my family for a few days and had the pleasure of perusing through my old Animorphs collection for the first time in quite a while. While I was there, I reread The Hork-Bajir Chronicles and The Andalite Chronicles back-to-back.
I have to say that especially when read in conjunction like that, they stood out sharply to me as being the best two books of the series. One thing I really loved about them was the thematic parallel between Seerow committing the crime that basically doomed the Hork-Bajir and came to be known as Seerow's Kindness, and Elfangor doing the same thing at the end of his own life which ended up essentially saving Earth. And aside from the doom of the Hork-Bajir world and the salvation of Earth, the same act also spawned the rise of Yeerk empire and its eventually downfall. I don't know why, but I found this parallel very moving. It spoke volumes about how this sort of thing has no inherent right and wrong, and sometimes it's impossible to know for sure how your action is going to affect the future - but sometimes the only choice is taking the chance.
Sorry for the ramble. Aside from the Chronicles, my other favorite books in the series are the 3 in the David trilogy (especially the last one), and #45. The David trilogy was the first time in Animorphs where I sat back and said to myself, "Damn, this is some heavy stuff." What David did to Saddler and his family is still, to me, one of the most screwed up and wrong things that happens in the entire series.
I loved #45 because Marco is such a great character and it was amazing and truly heartwarming to see him finally accomplish the goal he had been trying to achieve for literally the last 40 books. As someone else pointed out, it was also truly the turning point for the series, the book that marked the beginning of the end.