From a Megami reader's poll. Homura and Madoka take first place with more than double the votes of second place.
1. Homura x Madoka, Madoka Magica
2. Hibiki x Kanade, Suite Precure
3. Jintan x Menma, AnoHana
4. Okabe x Kurisu, Steins;Gate
5. Sakamachi x Subaru, Mayo Chiki!
6. Tooru x Run, A Channel
7. Margot x Malga, Kyoukai Senjou no Horizon
8. Mikoto x Kuroko, Railgun
9. Yuuji x Shouko, Baka to Test to Shokanjū
10. Kyouko x Yui, Yuru Yuri
Madoka Magica's OP song Connect came in second place for the year, in a close race with first place ranking Idolm@ster's "Ready!!"
Madoka and Kyoko are listed seventh and eighth in this character poll.