Tsukiko from Henneko.
Cutest anything in the universe.
Kobato comes second, she is also very adorable.
EDIT: After giving it more thought (as well as rereading the topic description again), only cuteness won't count.
1. Nico Robin (One Piece): She's an archaeologist, she has a bloody sense of humor, and her devil fruit powers are unique and awesome.
2. Ai Haibara (Detective Conan): She is a child genius, acts dangerous and cold, but is really sweet inside, and is secretly an eighteen year old on the run from an organization that wants to kill her
3. Tsutsukakushi Tsukiko (Hentai Ouji to Warawanai Neko): She's adorable, has a sweet tooth and enormous appetite, and a kuudere not by choice.
Cutest anything in the universe.
Kobato comes second, she is also very adorable.
EDIT: After giving it more thought (as well as rereading the topic description again), only cuteness won't count.
1. Nico Robin (One Piece): She's an archaeologist, she has a bloody sense of humor, and her devil fruit powers are unique and awesome.
2. Ai Haibara (Detective Conan): She is a child genius, acts dangerous and cold, but is really sweet inside, and is secretly an eighteen year old on the run from an organization that wants to kill her
3. Tsutsukakushi Tsukiko (Hentai Ouji to Warawanai Neko): She's adorable, has a sweet tooth and enormous appetite, and a kuudere not by choice.