It depends what I'm writing, but I like to choose names that fit the theme of my story, which isn't often easy.
In The End, the characters were named to fit the pokemon they were given to - Cleo is a meowstic, so I chose a cat name; or Tantrum for a vigoroth. Other names, like Sandpaw, just sounded like they were suited to an animal, whereas Hope and Faith were named as such because it fit the overall theme of the story and they were pretty important characters that helped point the plot in the right direction.
In Glitched, every character is named after computer, technical or mechanical terms. So are the locations (while also having the occasional Gen 1 reference hidden away). This is quite the challenge, I have to say.