I nickname anything I intend to use or just like, the only ones that go unnamed are 'dex fodder.
Used a theme once, Zelda for HeartGold - Link (Meganium), Sheik (Umbreon), Zelda (Espeon), Ordona (Ampharos), Morpha (Gyarados), and, uh, Helmaroc (Ho-Oh). Few others, too - I had an HM slave Wooper named King Zora.
Others are random associations, shortening their name (like Luca the spectacularly uncreatively named Lucario), or, "Well, they LOOK like a __". Did keep some fandom names, like Ganon the Emboar. Or memes. I will confess to Smugleaf and Wotter.
Just by way of example, my three most-recent teams: White - Smugleaf (Serperior), Nazca (Sigilyph), Tula (Galvantula), Darunia (Darmanitan), Kokoro (Krookodile), and Big Momma (Beartic). White 2 - Wotter (Samurott), Luca (Lucario), another Nazca and Ordona, Tai (Absol, from taijiki, the yin-yang symbol - I'm actually kind of proud of that one), and Rava (Flygon). And my White replay had Ganon (Emboar), Mirabelle (Lilligant), Sammy (Scrafty), Jellybaby (Reuniclus), Ellie (Eelektross), and Goose (Golurk).
Other names that I quite like that I've used in the past: Aultaria (shiny Altaria), Fi (Lilligant), Tatsubasa (Salamance,combined tatsu, dragon, and tsubasa, wing), Nordlys (Glaceon, Norwegian for northern lights, hatched and trained while in Norway to see the northern lights), Deku (Torterra), Fairyfloss (Clefairy), Hulk and Hulkish (Slaking and Vigoroth), Oregano, Paprika, and Peppermint (elemental monkeys), You Fucker (Shuckle, dear GOD it took a long time to find, several Tropiuses (Tropii?) all called Neckbanana, Myrtle (Tyranitar, she looked like a Myrtle!) and her Larvitar Minty, Argyle (Sawk), Tofurky (Vullaby), Beelinda (Vespiquen), Ghirahim (male Unfezant), Phantom (Masquerain, painted faces on parade!), Loveless (Cyrogonal), Miku (female Farfetch'd), Arti (Leavanny), Helios and Selene (Solrock and Lunatone), and Poliwrath named Hestor. He looks like a Hestor...
