I used to not like nick naming my Pokemon (except for my first one, a Turtwig I accidentally nicknamed "Turtwig" which stuck with it all the way through evolution), since I found it kind of strange. That changed completely though, when I started Nuzlocking. Ever since, I've nicknamed practically every single Pokemon I obtain. Sometimes the name is a reference (often convoluted), and sometimes just based on what sounds fitting for them.
Take my Black 2 team for example:
Freddie the Serperior - It's a regal Pokemon, and Freddie Mercury was the lead singer of Queen
Emanuel the Lucario - Caught him on Christmas morning
Marie the Ampharos - Electrocty made me think of science, and since she was female, I named her after Marie Curie (yes, I know she was a chemist, but still)
Richard the Arcanine - Named after Richard Parker, the tiger from the book/movie Life of Pi
Gaea the Flygon - Named after the Greek Mother Earth... thing... or whatever
Asimov the Golurk - Named after the famous sci-if writer, since Golurk's a robot
So yeah, nicknaming for me has become almost a bit of a hobby. I'll find myself sitting on the nickname screen for a half an hour at times, deciding what to choose for a name.