I have a "Furies" trend:
Alecto - Sneasel
Tisiphone - Froslass
Magaera - Mismagius
In addition to that, I also name almost all my pokemon after people from Greek/Roman myths (sometimes history). There are some exceptions...
Reglius the Scrafty. I named him after Regulus Terentius (I had a crap TV and couldn't see the letters very clearly), who was the Count of Bravil in Oblivion.
Alchemilla the Makuhita. Granted, Alchemilla is a PLACE not a PERSON, but it is the Hospital in some Silent Hill games.
Happy Jack the Machoke. I named him after the The Who song of the same name.
Faust the Pikachu, after Faust, the main character of Goethe's work of the same title.
Ickis the Sableye, after Ickis on Aaahh! Real Monsters
Oblina the Gothitelle from the same series
Moltar the Pawniard after Moltar from Space Ghost: Coast to Coast
Brak the Meowth (see above)
Zorak the Scyther (see above)
Smile.dog the Mightyena for obvious reasons
Mephistopheles the Houndoom. In Goethe's Faust, Satan (aka: Mephistopheles) takes the form of a black dog coming out of a corn field.
Gamma the Toxicroak (though now, Seismitoad would work better) after Hunter Gamma from the Resident Evil Games
Rocco the Breloom after Rocco from "Rocco's Modern Life" as Breloom seem to be some sort of mushroom wallaby to me
Papre the Dragonite after "Dragonne Papre" mentioned in "Starlover's Log" in Morrowind (I think there is also a copy of it in later games. It is a book in reference to Battlespire, another game by Bethesda)
Llorona the Gardevoir after the La Llorona myth
Calcobrena the Banette after the Calcobrena boss from one of the early Final Fantasy titles, and the Calcobrena myth itself
Ultrmegchk the Skarmory after Ultra-Mega Chicken from Aqua Teen Hunger Force
Uzumaki the Igglybuff for...well, if you get it, good. If you don't and aren't used to scary images, I suggest you don't go look it up.
Kappa the Golduck after the Kappa myth
UncleDolan the Ducklette after Uncle Dolan. If you don't know who that is, don't go look it up. It's NSFW
Boba Fett the Cubone because Cubone wears its dead mother's head, and Boba Fett wears his dead dad's helmet
Zam the Zangoose after Zam Wesell. Don't know why.