Yodobashi Camera in Sakae also has a nice big selection (along with some actual English-language stuff) and a 10% point card to boot. That and Joshin (which also has a point card) are probably your best brick-and-mortar stores in town in terms of on-the-shelf selection, although I don't know if they'd order stuff for you and they're not FLGS's in terms of play support. Yellow Submarine will order in for you, I think, and one of our local members is trying to organize Kill Team events there, although all their game tables are currently given over to card games as it stands, but their actual selection is much thinner than either Yodobashi or Joshin. All three shops don't have any discount beyond the point cards.
The other shop Primarch was thinking of is Meruhen (
http://midoriku-style.info/archives/422), and it's probably your best bet in public-transport-accessible Nagoya if you want to actually order stuff instead of hoping for the best with what's in stock - they also have a 20% discount, I believe. Their stock on the shelves is not fantastic, though.
If you have transportation options to get a bit further afield, Plamojuku (
http://gorakuou.net/blog/index.php) is a tiny little shop up in Ichinomiya (although he's opening a second shop closer to Gifu station, I believe) that doesn't really carry stock on the shelves but will order in for you at a discount, and is actually proactive about supporting gaming in the store - I'm part of a small but very enthusiastic gaming club based in the store.
That said, I'll endorse Ring Tail too if you want to mail order. Good guy, and you can even pay by bank transfer or COD if you like cash.