Well, there was the Christian Arc in Kenshin, which deals a lot with persecution and religion differences. Aside from the ones that are already listed, I don't think I can think of any others.
EDIT: Well, I've never seen Full Metal Alchemist, but doesn't it contain references to The Divine Comedy? Which includes references to Dante's Inferno and the 7 Terraces of Purgatory (or 7 Deadly Sins), which are references Christian themes.
(reference link)
Well... this isn't anime, but does this count as Christian-related?
http://www.youtube.com/watch?v=tnp0ltpEfpQ
EDIT: Well, I've never seen Full Metal Alchemist, but doesn't it contain references to The Divine Comedy? Which includes references to Dante's Inferno and the 7 Terraces of Purgatory (or 7 Deadly Sins), which are references Christian themes.
(reference link)
Well... this isn't anime, but does this count as Christian-related?
http://www.youtube.com/watch?v=tnp0ltpEfpQ