Oh, man, I nickname my Pokemon all over the place. I love nicknaming them and will spend hours leaving the game paused and thinking about or researching the perfect nickname... if I haven't already done that ahead of time. Let me organize the notable ones here along with my logical reasoning for them.
-My Best-
Serperior:
"Ouroboros" - Symbol of a serpent eating its own tail that signifies the cycle of nature... thought it fit the grass snake.
Hypno:
"Nietzsche" - Unusual name, and the name of
a dude that fits Hypno, so I thought it was perfect.
Sandile:
"Kremlin" - Play on the Kremlings from Donkey Kong, but I preferred the spelling of the Russian building, so I went with it.
Magnemite:
"Viktor" - Metal and electricity make me think of Victor Frankenstein, but it also just sounds hilariously fitting on its own.
Woobat:
"Valentino" - Self explanatory if you know anything about Woobat.
Pidove:
"Wright" - Sounds fitting to me, plus Wright Brothers and airplanes and whatnot.
Vanillite:
"Häagen-Dazs" - Based on
the brand of ice cream. I don't use Vanillite though.
-Mythology References-
Houndour:
"Barghest" - Named after the monstrous black dogs of English folklore.
Yamask:
"Ah Puch" - Often mentioned among Mayan death gods, though not actually a proper name for one.
Arceus:
"Grigori" - Named after the angels who came down and became infatuated with human women.
Elgyem:
"Voronezh" - Named after a city in which there was an alien encounter story that I feel describes similar creatures.
-Pop-culture References-
Trubbish:
"Wreck-Gar" - The
Junkion character from Transformers.
Blitzle:
"BrightEyes" - A classic My Little Pony character.
Duskull:
"CandleJack" - From Freakazoid.
Liepard:
"Panter" - Based on
Panter Flauclaws from Mega Man Zero 2.
-Other Notables-
Venipede:
"Atropine" - Just named after a poison that comes from a plant. Thought it sounded cool.
Maractus:
"Chalina" - Sounded... "ethnic" and like it fit my female Maractus. =P
Porygon:
"Foobar" -
Programming term that I thought sounded perfect for the derpy-looking little guy.
Watchog:
"Vanguard" - He looks ready for some serious ****, so I wanted him to have a bad*** name.