I really like 'Alphonse's Redemption'. In this fanfic, Alphonse goes on a quest to make amends for things he feels guilty about. The author does an amazing job of expanding on his relationships with other characters in a believable way.
There's also 'A New Alchemy for Alphonse'. This one takes a creative approach. It shows Alphonse exploring new forms of alchemy that are not in the original story. It's full of interesting ideas and the way it portrays Alphonse is both engaging and true to his nature.