Willie's is your classic vintage store. LOTS of super cool old stuff as well as new stuff. You def, want to go there!
You might Dig Capitol guitars in St. Paul. They are more of a heavy rock, shredding store.
American guitar, from what I understand, specializes (or specialized..never been there) in more high end built stuff. I know they do new as well. Can't say anything about whether they do vintage.
The podium is pretty much the place to go for acoustics.
Hoffman guitars is where you want to go if you want to see a hoffman guitar. That's really about it for them. Unless you are getting something repaired, or want to play one of Charlie's guitars, there isn't any need to go there.
I've never been to twin town, but they have their following.
You might also check into solidbodyguitar.com (I think that's their website.) I know there were rumors of Bruce packing up the business...he might be appointment only...not sure. But worth checking out as he usually had some cool stuff too.
That's all I'm really thinkin' of for REALLY cool stores, not saying there aren't potentially others...like foxtone, or the new guitar mouse stores, but I don't know that they'd have what you're looking for.
P.S I"m the guy that used to work at willie's.
