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Good on you for vetoing Link Gannon; the lad may have grown up to be constantly torn between saving and destroying the world. /stupid joke.
In all seriousness, Lincoln/Linc is a lovely name, and with more than one extremely admirable namesake, to boot. Good on you!
As a lover of video games, I think it's absolutely fine to name a child after a character you are fond of/wish them to emulate. I probably would keep it to names that have a history as "normal" names though: i.e., Alistair, Dante, and Zelda are acceptable, whereas Sephiroth is not.
I was going to say that it's because people feel freer to give outlandish names to characters, but then I remembered that people give their kids bizarre names, too...
Yeah. I guess I don't really have an answer there. But I do get where you're coming from.
All of my guilty pleasures are sci-fi/video game references. Most egregiously, Jadzia (Deep Space Nine) and Leliana (Dragon Age), which are completely made-up, and which I doubt I would actually bestow upon a child, though cats and dogs are fair game.
Luckily for me, though, the rest of my nerdy picks are perfectly acceptable "real names" like Tali, Samara (Mass Effect) and Kira (anglicized form of Ciara, which can also be a DS9 reference spelt this way).