I use two methods, depending on the story type. If I want natural-sounding names (which fit most of my stories), I troll around the online lists of names looking for a combination that sounds like a name a mother would give her child (so, no "Stockwell Simeon"-type names in my stories).
For adventure fare, I will often choose a name that is more dramatic, like "Kestral" (small bird of prey, good for a heroine), find a complementary first or last name, like "Carolyn," and I'm good to go. I do enjoy the extra leeway you get when writing an SF or fantasy story, and I have taken full advantage there, creating names that fit alien characters and futuristic but still human-sounding names.
But I always stay mindful of going too far overboard, lest the names start to sound too over-the-top in aggregate, or so hard to type or pronounce that they interrupt the flow of reading (or writing).
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