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By their first name most of the time, however if they are usually referred to by their surname in the series then I'll probably call them by that, as I'll be used to it. A prime example of this is Harima from School Rumble.
Whatever comes to my mind first usually. Japanese names are hard for me to memorize, so whenever I'm talking about a certain anime/manga/game character, I just refer to them by the name that comes to my head first. XP
I use the most commonly name they'll be called by. I never tend to use the last name 'cause if I did,no one would recognize who i'm talking about sometimes.