Death Note has a dose of gloomyness and "cold attitude" going on trough a lot of the show, which I'd assume can be considered "dark". I'd suppose the pretty greytoned animations helps a lot in visualizing a dark atmosphere too.

Never watched FMA, so I can't say anything about that one. But from the screenshots/clips I've seen, I've always thought it was indeed more of a humor-filled kind of show than an anime with a dark atmosphere. =O