From data I've collected on this board and the ISML forums (48 nominators), here are the Top 66 nomination getters:
Homura takes first place with ease. I'm quite surprised at the amount of nomiantion support she's receiving.
Kurisu also ends up quite far ahead of everyone else. After her loss to Aria in an exhibition match, I didn't expect her to be this popular.
Sena would have been my guess for highest nomination count and she comes in at a distant 3rd with only 1 more nomination than Yozora and only 2 more than Kobato. I wonder if some people here opted to not nominate Sena because they thought she would get in easily. Madoka and Kyouko from Puella Magi Madoka Magica fill out some of the other top slots along with Erio and Ika-Musume.
The Stella character with the highest number of nominations in my sample was Kawasumi Mai. This is due a bias in the sample. The real highest nomination getter in Stella looks to be Sakagami Tomoyo or Holo.
Miki Sayaka seems to lack support relative to the other Puella Magi.
Not on the list is Kanzaki H. Aria with only 2 nominations from the 48 nominators. Maybe she's just not popular with the nominators on the boards I looked at but I expected a bit more from her.