I'll try to make this list as least biased as I can. And by that, I mean even if I dislike the anime, I'll still add the character to the list if I think it's a good character. Of course I can only add characters from the anime I've watched so it might seem really restricted.
5. Taiga Aisaka (Toradora!); To be honest, she's just another common tsundere, but the set-up of the show's central plot seems to help this character's motivation and development.
4. Azusa Nakano (Keion!); She is distinguished from the rest of the main characters and has a reasonable mind that seems to not fit in as much with the rest of the crazy 'world' around her.
3. Kagami Hiiragi (Lucky☆Star); It felt like she was created as a character foil to Konata, and that adds a lot to interaction between the two. As a character by herself, she isn't all that special, but the way she interacts with different characters shows her personality being more looked upon. Moreso than the other characters.
2. Haruhi Suzumiya (Haruhi Suzumiya); Kind of against putting three tsundere on the list, but talk about an interesting character. The moment you get any infomation about this character it just grabs your attention. I haven't read much of the novels, but the anime shows that this is a character done right. What's going on in her mind is what drives this series and is an interesting experience.
1. Tomoya Okazaki (CLANNAD); I liked the development of his character throughout the series and has the most realistic personality out of the characters. I could probably bunk the heros of Kanon and possibly AIR into this category also, but I think if anyone comes out on top, it's Tomoya.