I usually give them pet names, like things you would call a significant other (Cuppycake, Cuddles, etc)

I usually give them pet names, like things you would call a significant other (Cuppycake, Cuddles, etc)
They're pretty much random... However for my SoulSilver party half of them (who also happen to be starters from various generations) are named after Warcraft-characters. Several other Pokèmon caught in SS has gotten that too:
Sylvanas the Feraligatr (because it was totally unexpectedly female!)
Thrall the Torterra (because its green)
Krasus the Charizard (because its a red dragon)
The rest of the party are
Chuckie the Ampharos (named after another amphy I have on Colloseum, named ChuckNoris for some random reason)
Percival the Gallade (thought of something "knight-like". Originally considered Galahad but Percival was cuter:B)
Rouge the Weavile (I don't know why. She just needed a name. )

There aren't really many nickname themes I use, except for pokemon I'm trading between my versions to transfer. I've called a Budew Tradew hahha. But I'm using Greek gods/goddesses for my Eeveelutions!
My favorite shinies. :3
Well, in my games I just name them stuff. (Colonel) Saunders the Blaziken, 1UP the Shroomish, Palindrome the Muk, Mothra the Butterfree, etc. (I try to keep them mildly humourous... I kind of fail.)
However, my URPG mon are named after places. At the minute I have Cairo the Riolu and Babylon the Shieldon, but I intend to get Alexandria the Ampharos, Salem the Espeon, and Tokyo the Tyranitar. (LOL Godzilla)
Look at my tiny avatar and right-aligned signature.
Gaze upon them and tremble, for they are good.
It is good to have friends, is it not? Even if, maybe, only for a little while...
I name my Pokemon after people I know.

I tend to go with Greek god and goddess names.
I remember in LeafGreen, I named the Kanto Starters, as well as my Eevee and it's evolutions, after characters from Devil May Cry. In Hoenn, I just named each starter after the version who's colored they shared. In Platinum, I named the starters after character from the Japanese version of Journey to the West. In SoulSilver, I gave all of my team names that ended in -taro, in honor of the PokeSpe version of Gold. (The only exception was the lone female on my team, Natsuki the Ampharos.)
I haven't really been following any trend in GenV, I've mostly just been giving them whatever name seemed the most appropriate at the time I caught them, based on what I knew about their species. However, I did name my Zekrom Epyon, and if I ever get a Reshiram, I fully intend on naming it Zero, after the Wing-0 Gundam.
I have nicknamed all my Pokemon except junkers ever since the first gen. Not once have I ever noticed myself actually trying to name in a specific theme. I tend to base the names around the individual Pokemon and its line. Like, I have a Quagsire named Wally from SS, a Milotic named Venus from Plat, and a Kabutops named Slashmajig from Red.
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