Neera was the first pokemon I ever nicknamed. I fell in love with the name when I watched Dinosaur, and for some reason it seemed to fit Scyther perfectly. Alexis continued the trend.
Sneer's background is a massive tale in and of itself, but long story short, her name came from the nasty look she gave me when I rescued her from her abusive trainer. Narrow and the kids came from my wanting to match her theme.
Xinari is based off the espeon I have at VS, who is fabulous and a deadpan snarker when his trainer/brother *a Furry who fully believes he's an Espeon in a man's body* gets wound up XD
Mr. Moose is named that way because Terrakion looks like a moose to me, and it makes people laugh.
Angel is named after the Absol you get in Red/Blue Rescue team, who I named Angel because the first time I played through it, I was getting my ass kicked left and right because I couldn't bring a 3rd member with me, and she suddenly appeared and helped me, and was a HUGE help.
Basile is named after my best friend/sister, as Lugia is her favorite legendary
Ranny is named after a friend of mine from Pokefarm, who summoned and hatched my Suicune Summon for me
Pendra, Diaruga, and Parukia's names are all derived from their Japanese names *or in the case of the latter, pronounciation*
Mosaic is named for my partner in Explorers of Sky, also a Shinx-now-Luxray
Flower is named so because her character, the Haxorus she's based off of, is incredibly timid/shy and prefers to spend her time in the garden, taking care of the plants.
Ming-Ming was named so because when I first saw her as a Stunky, I squealed/cried from how adorable she looked, and I wanted to give her a name that was just as cute.