I nickname some of my Pokemon. Pokemon Pearl was the only main Pokemon adventure game where I nicknamed my entire team.
Empoleon - Azuria (Az-err-ee-a)
This name is derived from "azure", which is a shade of blue.
Luxray - Raye (Ray)
Not hard to figure out where this one comes from - "ray".
Rapidash - Fiora (Fy-or-ah)
Derived from the word "Fire".
Bronzong - Iore (Eye-ore)
Derived from the words "Iron Ore".
Roselia - Botane (Bot-a-nee)
Derived from "botany", and is pronounced that way, too.
Drifblim - Ciela (See-el-la)
Yes, I know this is the name of the fairy in Phantom Hourglass. I thought of giving my Drifblim this name because "ciel" is French for "sky".
Cyndaquil - Flara (Flarr-ah)
This name is actually the shortened form of the name of a Mario character I once made up. The character was a fire-loving Toad whose name was Flara T. (based on the fact that most Toads in Paper Mario have "T" after their names). I thought this name would be appropriate for Cyndaquil, since it was Fire-type and female.
Chikorita - Cherri (Cher-ree)
I thought this name just sounded appropriate for a female Chikorita.
In Mystery Dungeon 2, I gave every single Pokemon I recruited a nickname. The legendary trio (Uxie, Mesprit and Azelf), like the other Pokemon, got nicknames, but I made them sound similar to each other to make them seem even more like a trio.
Uxie - Citronia (Sit-rone-ee-a)
Derived from "citron" which means "lemon", based on its color.
Mesprit - Cerisia (Sehr-ee-see-a)
Derived from "cerise" which means "cherry", based on its color.
Azelf - Azuria (Az-err-ee-a)
Derived from "azure". Yes, I know I gave my Empoleon the same name...