Thanks! I'm glad the list makes sense to people other than me. ;)

You're right that the Doctor's darkest moments are right after he's suffered himself. It's true in season one, too, with "Dalek," where the wounds of the Time War are still really fresh and he lashes out in a way that's kind of scary.

I like that he's not arbitrarily dark; it's something that's sympathetic and understandable, because it's a reaction to what he's experienced.