On rainy Saturday mornings I get a tinge of sadness. Not because the soggy SJ weather brings me down (although it does suck) but because it reminds me of when Christian and I used to go hang out at The Sorcerer's Stone. Although I didn't live here very long before the store closed I still developed an attachment to the place. (And it seemed like most of our trips there were on rainy Saturday afternoons, so it's an associative thing for me.) When The Sorcerer's Stone closed, and Joe died, it left a gaping hole in the uptown and in local "geek" culture. We don't really have an "old school" comic shop/hangout anymore. Sure, we have Mad City Comics but it's inside Read's/United Book Store, so it's not strictly a "comic shop". You can get comics and paraphernalia there, the staff are nice & you can hang out a bit (although it's not really conducive to long stays), but there are all these non-geeks coming in there buying cigarettes and trading in their musty paperbacks. Then there's Gamezilla, but it's way over on the West side, so it's doesn't have that "downtown" vibe that a true comic shop has. Plus, comics aren't the main focus of Gamezilla: they're secondary to gaming (TCGs, role playing, minis, video games, etc. are their main stock, then manga/anime their second focus, with comics probably coming in third). What Gamezilla does have going for it is that "clubhouse" feel, where you can go waste an afternoon hanging out with your friends, and again the staff is cool. Still, neither of those places is, in my mind, a "true" comic shop. I've been to a lot of comic shops and when I think back on the truly great ones, there are general characteristics that they all share.
When I think of what makes a great comic shop is a combination of nostalgia and the "underground" factor. This is one part the "musty, dusty" stuff and one part cutting edge. By "musty, dusty", I'm sure you know what I mean: basically what you might describe as "the old curiosity shop". Prized golden-age and silver age comics lining the walls (something to drool over and aspire to one day buying); rows and rows of long boxes of alphabetized back issues (for treasure hunting); and the "museum pieces", ie, assorted collector's items from by-gone eras like baseball cards and old toys (ie, things you wouldn't want to buy but enjoy looking at). The really good "old school" comic shops generally have this same look (kind of worn and dingy, downtown storefront), and yes a distinctive smell (very dusty and slightly moldy!). On the flip side, a good comic shop also needs an underground or "cutting edge" factor too. By "cutting edge" I'm referring to items that were more modern and had a quirkier bent to them. In this category are the "indie" comics, photocopied zines, strange import books, fan magazines devoted to really obscure topics, etc. These are the types of materials you'd never see anywhere else but a comic shop. You'd never be exposed to this type of stuff in a "mainstream" place like a drug store comic rack or a flea market table. These are what you might call the skeezier items: either too racy/controversial/violent or too obscure and fan-specific to be palatable to the casual consumer. With these items lay the possibility of discovering something new and interesting...or it might go completely over your head.
Finally, a third characteristic of a great comic shop is the "Cheers" factor. You know, a place where everybody knows your name. I touched on this earlier with Mad City and Gamezilla, but a comic shop tends to be a hangout for like-minded individuals (ok, "geeks") and there's a social aspect to shopping there. Any given time you visit the shop you're bound to see someone you know there. The workers know you, remember your tastes and interests, and they're usually free to sit behind the counter & chat. The best shops invariably have a character, a distinctive personality, that everyone associates with the store. In the case of The Sorcerer's Stone, it was Joe Harris. So, a great comic shop can be a kind of clubhouse, where you might go just to seek friendship not necessarily to buy anything. Even when you visit a comic shop in another city, you tend to see the same thing. You can almost spot the "counterparts" people have in other cities!
In Halifax it's Strange Adventures. In Bangor it's Topshelf Comics. In Toronto it's The Beguiling. No matter where you go, the feel is pretty much the same. Here it used to be The Sorcerer's Stone, and although there are some worthy successors, nothing has truly replaced it.