Hairy Tarantula is the one on Yonge, near Dundas. It has an amazing selection of everything, and a used book room in back. No cell phone policy bugs me, but they have a lot of reasonably priced trades (no loose issues, tho). It's not across from the HMV, tho it is near by. In fact, it's across from a massive, glowing lights strip club: turn away from naked ladies, and you end up in a gaming store; ignore the irony and buy stuff?
410 Yonge is near College, and has magic cards galore. it's well organized, and has monday night rpga (which I can never make it out to!). I end up buying stuff there, as it has a good selection and prices on 4e stuff. Upstairs gaming tables out the wazoo.
One Million Comics: no rpg stuff, north of 410 on Yonge, south of Gray Region. Good comics and amazing statuettes and t-shirts, and genuinely friendly staff (ignoring the fact they seem like mobsters; they're just Italian).
Gray Region sucks. They had bad customer service, and the gaming room was simply a pile of non-rotating stock from the early 90s. Prices were way inflated, and I constantly felt gauged. Only the minis were ok, but that's if you like painting metal minis from obscure companies (which I would, if I painted minis). I found a copy of Rober Jordan's Wheel of Time d20 there, among some old Al Qadim 2nd hand modules. Yeah, old.