Dawn's Buneary.
That Togepi. From where No Togepi has Gone Before.
Ash's Tsutarja.
Those are the 3 Pokemon that have shown Pikachu is male.
Seriously, why would anyone think Pikachu is female? Pikachu's entire demeanor just screams boy and you'd seriously have to be slow or something if you can't get that.
That's like saying his Charizard is female, when you can tell just how it acts, that its a boy. It falls in love with Charla, yet no one is wondering if Ash's Charizard is female. Squirtle and Bulbasaur, two more examples and all obviously male, you can just tell because of how they act. Now, out of all Ash's Pokemon, Pikachu is the one everybody and their grandma can't seem to figure out, yet its so painstakingly obvious it hurts. Regardless of the gender additions that appeared during Sinnoh. You'd really have to be blind or something to not know Pikachu was a boy let alone just assume he was, due to the way he acted.
So he cross dresses a couple of times and the entire world is going crazy cause they can't figure out the gender of the rat. Ash does too and its played for laughs. Pokemon probably look good in anything anyway. Fact of the matter is, Pikachu is entirely male. :/