I hate having to pick THE favorite - there's so many to choose from! - but I think the Ghost in the Shell series is probably at or near the top of my list.
I've also really liked (in no particular order) Haibane Renmei, Shakugan no Shana, Mushi-Shi, all the Haruhi Suzumiya episodes and movies (except maybe the infamous "Endless Eight" arc.. OMG!), Clannad: After Story, Lovely Complex, Spice and Wolf, Natsume's Book of Friends, Angel Beats!, Usagi Drop, Humanity Has Declined (the banana episode always makes me lol), the Bakemonogatari series, Shigatsu Kimi no Uso, Shin Sekai Yori, Kokoro Connect, Pet Girl of Sakurasou (first season anyway), Kotoura-san, Blue Spring Ride, Grimgar of Fantasy and Ash. Also all the Ghibli movies.. I just watched Whispers of the Heart again a couple weeks ago, but also Spirited Away, My Neighbor Totoro...
So, so many more.. Hard to even make a top-10 list! I know I'll think of more as soon as I post this too.