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...
Once named a Snorlax Queen Chub because it was female. (The name I had in mind was for a male Snorlax)
Also named my Tepig Bakugami. If you don't know what that is, then you haven't played one of the best games of all time. --- "If speed and deadly accuracy had children, I'd be their favorite!" -Sniper (MNC/SMNC)
Oh, yeah, I also named a Snorlax "Igordão" (that was the portuguese name for "Fat Bastard", the villain from Austin Powers). --- "If you want to know what a man's like, take a good look at how he treats his inferiors, not his equals." -Sirius Black