I figured I'd make my first post here something useful and do a more comprehensive write-up of Vienna's many perfumeries, since the information so far has been a bit scattershot and incomplete. I've been living in Vienna for six years now, so this should cover pretty much everything noteworthy.

I've highlighted my personal recommendations in red.

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First, the large fragrance chains:

Douglas "House of Beauty" (Kaerntner Strasse 7)
Douglas is the largest cosmetics and fragrance chain in town. Most of their stores don't carry anything interesting for aficionados, but their flagship store on Kaerntner Strasse has an impressive selection of mainstream/designer scents (from cheap brands like cK all the way to Tom Ford) with a few niches in between.
Brands (selection): Guerlain, Chanel, Hermès, Jean Patou, Jo Malone, Tom Ford, Creed, Acqua di Parma (upstairs!), Zegna (boutique line), Boss (boutique line), Bond No. 9, and many more...

Douglas (Kaertner Strasse 26)
This Douglas store is noteworthy for selling Chanel's "Les Exclusifs" boutique line.

Marionnaud (Kaertner Strasse 19, inside the "Steffl" department store)
Marionnaud is another mainstream cosmetics and fragrance chain. Their Steffl store is probably the largest and most interesting. Mostly mainstream brands, with a few niches (Creed, Serge Lutens, Juliette has a Gun).

L'Occitane en Provence (Seilergasse 1)
International chain selling its own brand of fragrances. Several stores in town.

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Now to the more interesting stores:

Le Parfum (Petersplatz 3)
Vienna's prime address for all things exclusive. Wide range of niches and high-end designers. Most notably, one of the few stores that sell Guerlain's boutique fragrances (Derby, Chamade etc.).
Brands (selection): Guerlain, Tom Ford, Robert Piguet, Byredo, Caron, Amouage, Montale, MFK, Parfumerie Generale, Aedes de Venustas, Annick Goutal, Frédérick Malle, Serge Lutens, Armani Privée, Clive Christian, and many more...

Nägele & Strubell (Graben 27)
High-end cosmetics chain that runs several stores in Vienna. Varied selection of upscale mainstream and niche fragrances.
Brands (selection): Guerlain, Hermès, Atelier Cologne, Moresque, Acqua di Parma, Annick Goutal, Creed, Penhaligon's, Juliette Has A Gun...

Kussmund (Habsburgergasse 14)
Some well-known niches, but mostly focuses on newer (2000 onwards) niche brands.
Brands (selection): Parfums de Marly, Phaedon, Memo, Jacques Zolty, Terry de Gunzburg, Laboratorio Olfattivo... also Dyptique, Santa Maria Novella

Le Parfum, Nägele & Strubell and Kussmund are all under the same ownership (the company that also runs ausliebezumduft.de).

Filz (Graben 13)
Very old-school. Mix between traditional perfume houses and niche scents. Unfortunately, most fragrances are behind the counter, so care-free browsing without the SA is not possible.
Brands (selection): Guerlain, Balmain, Acqua di Parma, Serge Lutens, Annick Goutal, Chanel, Hermès, Lalique...

Duft & Kultur (Tuchlauben 17)
Boutique for everything fragrant; mostly soaps, candles, and home fragrances. Small but well-selected range of classic niche brands.
Brands (selection): L'Artisan Parfumeur, MPG, Annick Goutal, Parfums de Nicolai, Parfum d'Empire, Eau d'Italie, Creed, Fragonard, Etro, Dyptique...

Emis (Tuchlauben 18)
Just opposite Duft & Kultur. Fashion boutique selling Japanese designer clothing. Full lineup of Comme des Garcons and Yohji Yamamoto fragrances.

Maison de Parfum (Kaerntnerstrasse 10, Top 17)
www.maisondeparfum.at/en (note: they've been downsizing their online shop - the actual store has much more variety than the website)
High-end perfumery wedged in between cafés, so well-hidden that I literally walked past it for five years. Specialises in the luxuriously expensive. Notable for carrying many young niches (2010 onwards) and many middle-eastern houses.
Brands (selection): Tauer, Roja Parfums, Nabeel, MiN New York, XerJoff, Mona di Orio, Le Galion, Parfums MDCI, The Different Company, Vero Profumo, and many more...

Le Dix-Neuf (Seilergasse 19)
Tiny perfumery carrying high-end niche houses.
Brands (selection): Parfumerie Generale, Histoires de Parfums, Amouage, Montale, Nasomatto, Carner, Linari, Rania J...

Esbjerg (Krugerstrasse 7)
Grooming and skin care products mostly aimed at men. Selection of traditional "barbershop brands".
Brands (selection): Penhaligon's, Geo F. Trumper, Taylor of Old Bond Street, Truefitt and Hill...

Topsi (Kärntner Ring 5-7; inside the "Ringstrassen-Galerien" department store)
High-end cosmetics chain with several stores throughout Vienna. Mix of mainstream and niche scents.
Brands (selection): Chanel, Guerlain, Berdoues, Comme des Garcons, Serge Lutens, Bond No. 9, MFK, Penhaligon's, Amouage...

Stattgarten (Kettenbrueckengasse 14)
Charming boutique selling cosmetics, home fragrances and niche scents. Some well-known houses, but also a lot of smaller brands that you can't get in Vienna's other perfumeries. At time of writing only a reduced lineup due to store restructuring.
Brands (selection): Parfums de Nicolai, Parfum d'Empire, Etat Libre d'Orange, Institut Très Bien, Neela Vermeire, Andrée Putman, Sigilli, Oliver & Co., Miller Harris, Acqua di Genova, Eau d'Italie...

Le Visage (Mariahilferstrasse 1d)
Another traditional perfumery with a selection of mainstream and niche fragrances. Beware of the owner - he's an old-school salesman, and he's very good ;-)

Verinas (Franziskanerplatz 6)
Bridal dresses and Puredistance fragrances.

(Wollzeile 4)
Natural cosmetics and health-related products. Small selection of niche fragrances.

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Furthermore, there's a variety of brand boutiques around Graben and Kohlmarkt. This is just a small selection of stores that have fragrances, some of them boutique-exclusive:

Hermès (Graben 22)
Highly recommended. Full lineup of Hermès fragrances, from their standard lines all the way to the Hermèssences.

Chanel (Tuchlauben 1)
The opportunity to try Chanel's Exclusifs.

Cartier (Kohlmarkt 1)
Discreetly tug a sleeve over your cheap Seiko and check out "Les Heures de Cartier" =)

Bottega Veneta (Tuchlauben 5)
The "Parco Palladiano" line.

Etro (Tuchlauben 5)
Full lineup of Etro's fragrances.

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With the exception of Stattgarten and Le Visage, all these stores are within comfortable walking distance from each other. Did I mention that Vienna is awesome?^^

Obviously, there are countless other perfumeries throughout the city. However, most of them don't carry anything that you couldn't also get at Douglas or Marionnaud, so I'm not going to list them here.

Happy shopping!

- - - Updated - - -

How could I forget...

Knize (Graben 13)
Check out one of the world's oldest haberdasheries and sample their famous Knize Ten.