I love drawing inspiration from literature, mythology, music, video game lore and anthroponymy in naming my Pokemon. Sometimes the names are chosen for their aptness for a particular Pokemon, and sometimes for opposite reasons, if they have a particular irony to them. In most cases I put a lot of thought into the naming of my Pokemon and have a lot of fun with it.
My Talonflame's name is Icarus, after the Greek mythology figure of the same name. According to Greek mythology, Icarus was a man who attempted to flee the island of Crete with wings made of feathers and wax. He was instructed by his father not to fly too close to the sun, but he did so anyways, which melted his wax wings and caused him to crash into the sea. Seeing as Talonflame is a fire-type bird, the name Icarus is a little ironic.
My Malamar is named Hermaeus, after Hermaeus Mora, the Daedric Prince of knowledge and memory, in The Elder Scrolls series lore.
My Bisharp is a female and is named Wilhelmina, which means "willing to protect" in German etymology.
Those are a few examples of the ways I name my Pokemon. :)