I don't know if I'd ever have the guts to name my (hypothetical) children after an obvious video game reference, no matter how much I love the series. It's kind of shame, since I actually really like the name Link; my favorite kind of male names are short, single syllable ones, and Link is definitely no exception, however I wouldn't make the whole "Lincoln" compromise.. not a fan of that name, oddly enough.
Zelda, also, is a beautiful name I would consider even without the game connotation, but again, not very subtle nowadays. I feel like as the series gets more and more widepsread, we're gonna see a bunch of little Zeldas and Links and Sarias running when our generation starts having kids. It's a nice thought, but could possibly be embarrassing or awkward for the child in question. I think I remember reading a snippet in GameInformer about a staff member who recently had a child who he and his wife named Atari :S I dunno about that one.
I actually recently learned that Zelda is of German / Yiddish origin. My friend told me the other day how her mom recently found out that her Hebrew name is Zelda, which is pretty cool. So it's a legitimate name (Let's not forget that princess Zelda was named after Zelda Fitzgerald) but I wouldn't want to be known as one of those crazy parents who give their kids silly names.