I used to name my pokemon after mythological figures exclusively, but I've been getting silly in my old age. I also have a tendency not to nickname legendaries:
HG Team: Pierre (Golem), Mr. Squishy (Tentacruel), Mr. Burny (Typhlosion), Blackie (Umbreon), Quack (Togekiss), Gorgonzola (Tangrowth)...