Fullmetal Alchemist, Kuroshitsuji Recommendations
I'm surprised nobody has recommended Kuroshitsuji yet as an alternate anime to FMA. While Kuro was produced by A-1 Pictures and FMA was produced by Bones, they've got a LOT in the way of similarities.
The story is set in England (well, FMA's Amestris is based off of England). The main character is a short teenaged boy with abnormal body parts is called a dog by the public (in FMA, 'dog of the military', in Kuroshitsuji, 'Queen's guard dog'). He's followed around by someone who is not your average human, and together they solve mysteries about their country.
Both of them have great comedy and endings that don't stick to the manga.
Both main characters have a quest that they want to achieve by any means necasare.
Both have lost something that made them to to venture into that mission.
Both use supranatural to achieve their purpose.