The Ellimist Chronicles,
The Andalite Chronicles,
The Hork-Bajir Chronicles,
# 31,
# 48 and #54 TIE
I don't really have any reasons WHY, but these are the ones that jumped instantly to mind. I never have a single favourite book, whether in THIS series OR overall, so the closest thing I have to 'favourites' are the first ones that come to mind.