As a Melbournian, and a niche enthusiast, I second a majority of the suggestions here.
Myer in the CBD, in the beauty hall, stocks Keiko Mecheri, Histoires de Parfums, Atelier Cologne, Caron, L'Artisan, Frapin, Parfum d'Empire, Carthusia etc.
DJs in the CBD carry Amouage, Robert Piguet, Acqua di Parma, Annick Goutal, Costume National, Tom Ford, Juliette Has A Gun, Lubin etc.
Mecca in both the Myer CBD and elsewhere usually stocks Serge Lutens, Le Labo, Tocca, Comme des Garcons etc.
Peony Melbourne in Auburn has a wide range of niche including Brecourt, Creed, Fragonard, James Heeley, Miller Harris, Pure Distance and The Different Company.
Klein's Perfumery in Fitzroy carries Penhaligon's, Tokyo Milk, Nasomatto, Acca Kappa, Carthusia, Demeter, Miller et Bertaux.
Paint n Powder in Bourke Street Mall carries some vintage and rare fragrances including Molinard, Caron and Guerlain.
Paint n Powder on High in Malvern is also worth a look. The woman that owns this store is friendly and helpful with a wide range including Creed, Guerlain and Chanel.
The Lab Perfumery in Carlton has a small but lovely range of Fragonard, Ineke and Miller Harris.
In Clayton, there is a duty-free store that carries many discontinued and hard-to-find fragrances like Alexander McQueen, Clinique Simply, Burberry Brit Red and Brit Gold.
Also JR's Duty Free in Swanston Street is a good place to test fragrances, and the last time I was there they had the limited edition, Eau de Fleurs range from Chloe.