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I name everything that has a gender an actual name of that gender, such as a female Kingdra i nicknamed Claire. If I can find a good reference, such as the one mentioned, then I'll name them that. If not, I just name them a random name. Genderless Pokemon I name their species name, but getting rid of the caps.
Not changing this sig until The Undertaker vs. Chris Jericho happens on PPV (started October 4, 2009)