I could almost predicate this result. The thread should be "Non-mainstream anime" cuz we all know the favorite mainstreams. And so, I don't include them in my favorites.
1. Lupin the 3rd: Fujiko Mine to iu onna
2. Sekirei
3. C: The Soul of Money and Possibility Control
I'm bad at ranking so those aren't in order and here are a few others
4. Hyouka
5. King of Bandits, Jing
6. Phantom Thief Kaito (It's not really an anime, it's a short series based on a character from Detective Conan but I still include it in my top list)
7. School Days
8. GoSick
9. Oda Nobuna no Yabou (waiting for season 2)
10. Sakurasou no Pet na Kanojo
And, mainstream list:
1. BTOOOM! (Desperately waiting for Season 2)
2. Death Note
3. Detective Conan/Meitantei Conan/Case Closed
4. Highschool DxD
5. Inazuma Eleven
6. Sword Art Online
If you're wondering why Fairy Tail isn't on my list, it's because I read the manga. Top manga:
Mainstream:
1. One Piece
2. Fairy Tail
3. Naruto
4. Kaichou wa maid-sama
Non-mainstream:
1. Minamoto-kun Monogatari
2. First Girl