According to poll conducted at Biglobe website, drama romance anime series  Ano Hi Mita Hana no Namae o Bokutachi wa Mada Shiranai (Anohana: The Flower We Saw That Day) topped rankings on best late night anime series with the best ending.

The anime featuring Menma and her friends lead the poll with 353 votes while slice of life anime K-ON! and romantic comedy anime Bakemonogatari were in second and third, respectively.

Rankings

1. Ano Hi Mita Hana
2. K-ON!!
3. Bakemonogatari
4. Clannad After Story
5. Puella Magi Madoka Magica
6. The Melancholy of Haruhi Suzumiya
7. Danshi Koukousei no Nichijou
8. Another
9. Ano Natsu de Matteru
10. Mahou Shoujo Lyrical Nanoha

Poll was conducted between May 6 to 13, 2012 with 3,056 respondents voted. List is limited to anime series broadcast at late night which were completed last April 2012.

Late night anime is a term used in Japan to denote anime television series broadcast late at night and/or in the early morning, usually between 23.00 and 4.00.  [Wikipedia]

[Source]