In the first Pokemon game I ever had (Yellow), I only nicknamed a small handful of my Pokemon. But after that, I nicknamed every Pokemon I had in every game I had. Sometimes I would name them after characters I created, quite a few in G/S/C are named after Digimon, and quite a few in Sapphire and Leaf Green have names in a language some people say I made up...
For example:
-In Gold and Crystal, I have three Jumpluff nicknamed Leafmon, Palmon, and Vegiemon.
-In Crystal, my Alakazam is nicknamed Mewtwo.
-In Silver, my Meganium is nicknamed Loatifir, after a Pokemon I created.
-In my old Sapphire game, my Kadabra was nicknamed Espa Roba, a minor charcter in Yu-Gi-Oh.
-In my current Sapphire, I have a Wobbuffet named Jessie and a Chimecho named James. (So I guess I have to one day rename my Beautifly/Skitty May and my Pikachu Ash.)
-In Sapphire, my Cacnea is nicknamed Ouch. In Gold, my Pinsir is nicknamed OUCH!!
-In Sapphire, my Banette is nicknamed Deatheater. In Gold, my Noctowl is nicknamed Voldemort.
-In Leaf Green, my Raichu is nicknamed Kazuminari, which in Japanese means "thunder mouse".
-In Sapphire, my Relicanth is nicknamed Baaransu. Relicanth's actual Japanese name is Jiiransu, but the "Jii" refers to an old man. Since my Relicanth is female, I changed the Jii to Baa, which refers to an old woman instead.
-In Yellow, I have a Lapras named Flipper. In Crystal I have a Lapras named Flipper Jr.
-All the Koffings and Weezings I ever had were nicknamed Cigarette, Marijuana, and Weedy.
-In middle school I hated a girl named Yesenia, so I named my Muk after her.