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From best to not as good as number 1.
1. Angel Beats
2. Clannad (including after story)
3. Phantom
4. Fullmetal Alchemist Brotherhood
5. Anohana: The Flower we saw that day
6. Naruto Shippuden (Despite all the fillers the actual story is really good)
7. Air
8. High School Of The Dead
9. School Rumble
10. The World God Only Knows

On a side note some anime that I know will make my top 5 after the shows finish are, Attack on Titan, My Mental Choices, and Fairy Tail. Naruto Shippuden gets an exception because of the long run of the show.