Voted for Okabe, Kurisu and Suzuha
Okabe
Okabe was one of the most interesting main characters I've seen. A really arrogant, proud and stubborn man, but he's really nice, selfless and helpful as well.
During the first few episodes I found him a but strange, especially his often 'fake paranoid' personality, but he really grew on me as the episodes went by. He really cares for his friends and would do anything to help them. Especially his relationships with Kurisu and Mayuri felt heartwarming.
It was interesting to see how he was able to switch between his serious and mad scientist personalities as well.
Kurisu
Kurisu really feels like the 'main girl' for the anime (and visual novel) to me. Fairly proud, arrogant and stubborn like Okabe, but just as helpful and selfless as seen when she constantly helps Okabe and especially when she is willing to sacrifice her own life to save Mayuri's. She has the tendency to act like a tsundere.
She puts a barrier around herself, which can only be broken by the people close to her. I think she was really lonely before meeting Okabe and co, probably because of the bad relationship with her father. She was really withdrawn at first because of this, but the real Kurisu came out eventually.
I think Okabe and Kurisu helped each other grow during the show and complete each other when they are together. I guess they seem more 'alive' when the other is around.
Suzuha
A tough girl, who had gone through hell, but managed to stay cheerful while trying to carry out her mission. Somehow she appealed to me right away and I hoped she'd play a big part in the story. Happy that she was indeed one of the 'keys' to victory.
I think she grew a lot during her time with Okabe and co as well in the social department. She wasn't used to a peaceful time and you could notice that she acted like a kid at times, because she didn't have a chance to grow up like normal kids. Although at the same time she was more serious and mature than the rest.