Noda or Yui from Angel Beats (Noda's a great minor character just for his comic relief, although he does have a side for sympathy; Yui, if I said anything I'd spoil the show, but THEM FEELS)
Edward Elric from Fullmetal Alchemist/Brotherhood (his character development throughout the entire show is just awesome, and how it builds into the ending was just brilliant)
Renton or Eureka from Eureka Seven (Renton's the classic example of lameass who becomes a badass hero, but it's done so well with his characterization, and Eureka reverse mirrors it, from being a cold badass, to being a confused girl who develops feelings)
Simon from Gurren Lagann (his characterization is fantastic, and how he grows to become the hero through such hardships was amazing)
Saeko Busujima from Highschool of the Dead (I disliked her the first time, but after going back through it, she's one of my favorites not because she doesn't have flaws, but how her flaws play into her character)
Naruto Uzumaki or Hinata Hyuga from Naruto/Shippuden (initially he starts out really goddamn annoying, but grows throughout the story; Hinata is awesome because 1. she's adorably shy and 2. she constantly strives to be better because of the one person in the world who matters to her)
Senji 'The Crow' from Deadman Wonderland (he's just too badass)
Black Star from SoulEater (I like him personally because of how he differs from other main characters/heroes, instead of constantly whining about needing to get stronger, he just straight up trains his ass off to become better, not to mention his partnership with Tsubaki is amazing)