I chose my first protagonist's name because when I imagined her she looked like a student I'd once had. Other characters' names must come from the air, because I couldn't tell you why I chose them. Sometimes when I'm done there are two that are too much alike, like Leo and Lee, so I go back and change one of them. I've mentioned before here that a character's name can turn a reader off. I've had people tell me a story bothered them because they didn't like or couldn't pronounce a character's name.
Barry Eisler, David Morrell, and Lee Child joke that your protag must have the initials J. R. to be successful (John Rain, John Rambo, and Jack Reacher, respectively), and certainly Jack and John are popular hero names. Names can suggest character: Amelia Peabody, Miss Jane Marple, and V.I. Warshawski all evoke a mood, a personality, a genre. A blend of the whimsical with the serious can be used to the author's advantage. Warshawsky's first name is Victoria; her middle name is Iphegenia. We don't wonder that she uses her initials. With caution we can get humor from a name: Marshall is the name of a new character on television whose job is ... U.S. Marshall. And it's probably no mistake that so many detectives have foreign, romantic-sounding names: Dupin, Poirot, and even Columbo.
So that answer to "What's in a name?" is "Something." The reader reacts to it. You're probably safe with the standard names, but you also run the risk of fading into the crowd. If you go the opposite way and choose odd names, you run the risk of irritating the reader: too cute, too difficult, too out there. I guess we must write the story and then see if the names fit. If not, adjust them. (Thank goodness for "search and replace!")