My general philosophy is NO EXPOSED WIRES. that includes stuff running to my iPod and such. I have seen a lot of people put it in the cubby right above the cup holders, you can't see it at all when you put it there, but its a little inconvenient, but I assume you have iPod control on the Nav system so It wouldn't be a problem.
another place is running a line under the center console and sticking it under the arm rest.
You can put it into the glove box, I guess it just depends on if you need to access the controls on the iPod or mp3 or whatever.