I usually name my Pokemon after mythological characters, gods or terms in other languages.
Hydreigon > Nidhogg : From Norse mythology the dread biter, the dragon who gnaws on the roots of Yggdrasil and survives Ragnarok to be the force of evil in the newly created world, post Ragnarok.
Volcarona > Sunna : Also, form Norse mythology the sun goddess of the newly created world said to shine brighter than her mother Sol.
Vulpix/Ninetales (shiny) > Inari : form Japanese Shinto and Buddhist religion is the god(ess) of food and rice harvest whose symbol/messenger is the white fox or kitsune.
Flygon (shiny) > Djinn : from Islamic mythology a spirit (of the desert sort of), Flygon's Pokedex entry describes it as a "The Desert Spirit".
Noivern > Shingetsu : means New Moon in Japanese. Noivern fly around on moonless night according to their Pokedex entry in X.
Dragagle > Kombu Ryu: kombu is a type of Japanese seaweed and ryu is dragon in Japanese; in other words "seaweed dragon".
Noivern (again) > Stile Nacht : "silent night" in German. As Noivern flies around in the night and attacks out of the darkness as Pokedex entry in Y.
Sableye (shiny) > Bort : bort is a diamond that is darker in color due to impurities. Bort diamonds are often used for industrial purposes (i.e. drill bits, abrasives and etc.).
Sableye (again) > Tommyknocker : Tommyknockers are small leprechaun or brownie like creatures that inhabit mines and make tapping or knocking noises often before a cave in. Can be malevolent and harmful or just mischievous and mostly harmless.
Just for fun nicknames
Gardevoir (male)> Divine : Divine was a drag queen from the 70's and 80's who played the mom in the movie Hairspray (also starring Riki Lake).
Goodra > Mooshy : I named this Pokemon Mooshy because as a Goomy it reminded me of those mooshy stress/gross out novelty balls. More of a texture or feeling that I imagined Goomy to have.
Altaria (shiny) > Q-Tip : because its cottony and yellow just like a used Q-Tip.
Talonflame > Millennium : because it's a falcon and I love Star Wars too. Put the two together and you get...
Sylveon > Pixie Stix : Pixie Stix are flavored granulated sugar candy in a paper straw which are sometimes fizzy or tingly.
That's enough for now...