Here's a page of links to shops I've found useful and interesting. I'll be adding to the list from time to time.

Acoustic Guitar Company Brighton shop with some of the best acoustic guitars and mandolins in the UK.
Acoustic Music Works Pittsburgh shop specialising in Collings, Bourgeois, Breedlove and other high end acoustic and resonator guitars, banjos and mandolins. Nice people, very reliable. Tempting website.
Bernunzio Vintage Instruments Vintage instruments, parts and ephemera.
Carmel Music Co. Dexter Johnson has been building, repairing, and restoring acoustic guitars and mandolins since 1969 and now specialises in the highest of high end acoustic instruments - including 'Herringbone' and '45' style Martins, D'Angelico archtops, Gibson built 'Lloyd Loar' F-5 mandolins, Strombergs, and various Larson Bros. creations. He commissions exotic models from Collings and others, usually employing Brazilian rosewood.
Coda Music Stevenage and Leicester company. Excellent range from beginners to high end.
Cotten Music Loads of top quality new and used guitars. Gets very good writeups on the acoustic guitar forums.
Dream Guitars Exclusive boutique store specialising in very high end small shop makers like Ervin Somogyi, Kathy Wingert, John Greven, Marc Beneteau, Dana Bourgeois, Ralph Bown, Charles Hoffman, George Lowden, Bill Tippin and Bruce Sexauer.
Elderly Instruments Vintage fretted instruments. Lansing, Michigan's finest.
Exceptional Guitars Eugene, Oregon specialist in fine new and vintage acoustic and electric guitars for players and collectors.
Folkway Music Ontario, Canada shop - nice site, has some very desirable guitars.
Gruhn Guitars George Gruhn is recognised as one of THE experts on vintage and collectable guitars. Gruhn Guitars was founded in Nashville in 1970. Always worth a look. No bargains here, but a fascinating website.
Hill Country Guitars Wimberley, Texas store. Excellent range and helpful to deal with.
My Favorite Guitars Jon Garon is the biggest exporter of Martins around the world. Very knowledgeable, thoroughly reliable to deal with and a nice website.
Oasis Music Nice store in Ringwood, Hampshire. Oasis Music sells new and used electric, acoustic and bass guitars by Gibson , Fender, Paul Reed Smith, Gretsch, Taylor, Martin, Guild and Collings and is the sole UK distributor for Huss and Dalton.
Retrofret Vintage, rare and unusual instruments.
Schoenberg Guitars Eric Schoenberg is a key figure in the renaissance of the acoustic guitar. His collaboration with CF Martin and Dana Bourgeois led to renewed interest in pre-war designs such as the OM-18 and OM-28. Interesting inventory.
Vintage and Rare Pricey but tempting. Well worth a browse.

Green metallic Strat

Martin OM-42s

Daphne Blue Strat

Vintage 50s Tele