Pretty sure this post has been done a few thousand times, but eh, I'll indulge.
Regular series, I love the David trilogy. #6 is also great, because it's the first time you get to see into the mind of a Yeerk, so to speak.
My favorite Megamorphs is #4, Back to Before. My favorite Chronicles, and overall favorite book of the entire story, is
The Hork-Bajir Chronicles (I'm bolding it because it's just that awesome). I'm also partial to Visser and TAC, though.