I've named any Magikarp I've ever caught Magikrap for obvious reasons.
I lost a battle due to my opponent using hacks, and was forced to give up my Mewtwo to the victor, so just to spite the cheating git I nicknamed Mewtwo S***biscuit before the trade so he was stuck with it.
I was traded a Wailord for unlocking the Regi's that the owner had named FailWhale.
Every now and then I'll name a random Pokemon 'OverThere'. Just so when used in battle I get such delights as 'Let's go, over there!'.
'Hey, that one wasn't my fault. They're twins. I'd had a lot to drink, they look really similar, and you know, sometimes the hand just slips...' - Long story...