Well, you can easily guess that my absolute no.1 is Homura. She's not perfect, she's not completely right in the head but hey, this is why I love her! I even have another version of her, a little different from her canon self but still very similar.
Then, let's see. The people she's closest to are my next two favs. Madoka is someone with a strong sense of responsibility. She can kind of complete Homura and they love very much and mutually support each other. Yeah, I know it's not a Rebellion fact
But I just can't (or don't want) to imagine the whole thing ending up like this. I think there's more to Madoka than she showed during Rebellion. Her plan was to save Homura and it hasn't failed - it just hasn't completed yet. Really, we're talking about a deity, not a 14-yo schoolgirl. I really think she was the mastermind behind everything that happened. It's possible that her sense of responsibility (for who she had tamed) made her give up her godhood but I repeat, I don't think it's the end of story.
Kyouko is in this tier too. In my works she's an "older sister" figure for the two little lovebirds (even though she's technically much younger than Homura at that point). It may be unexpected, she did surprise me too but this is what happened. In the original series she was the character that seemed hiding something (to me at least). She's wild and restless but has strong morality behind her street urchin mask.
Then come Sayaka and Mami. Mami didn't get enough screen time to get close enough to me so I feel her a bit of a stranger. Sayaka is very different. Her story played a very important role in the series (and her downfall was what got me hooked on Madoka Magica) but she could be quite annoying at times (looking from Homura's point of view that I assumed so easily...). So while Mami is kind of distant, Sayaka is ambivalent.