For me, naming male characters is more like choosing an everyman kind of name, something that the average reader can relate to. Most of the names I choose--Paul, Carl, Bill--sound average, whitebread, and the family names are invariably Christian sounding.
Please understand, this is not to knock anyone or start a holy war, LOL. But I've noticed that the majority of novels have names that sound like Christian ones, reflecting the majority of people within North America as well as the world. With Catnip and its sequel, Catnip 2: Rise of the Transgenics I deliberately chose a non-Christian sounding name for the hero--Goldman--and as to why, it just popped into my head, as all my characters' names do.
As for the women, a tad more difficult. If they're from Earth, again, I choose a fairly common name--Lindsay, Myra (sort of old-fashioned, but I like it), Megan, Amy, Anastasia from Catnip (she's of Russian descent) ...but for alien women's names, I usually end it in an -la...Angella, Angyalla, Shayala...sounds more poetic to me. Meddee (she's an alien but supposed to be somewhat like a woman from the Middle East) is the one no -la exception. I let my instinct guide me. If it sounds right to me, it's going to fit. If I dither over the choice, then it gets dumped and I think of something better.
Sorry for the long post.