Highly recommended: Parümerie Albrecht
There are two stores quite close to each other: Große Bockenheimer Str. 37 (the so-called "Freßgass") and in Goethestr. 27, which runs parallel to the former.
http://www.parfuemerie-albrecht.de/ for phone numbers and directions
Goethestr. features Malle as one of the few stores on Germany, then there's Lutens, Villoresi, Hugh Parsons, Floris, Penhaligon's, Clive Christian, L'Artisan, Creed, Diptyque, really pretty much every important niche and all the classics. What they don't have Kobberger does and vice versa. Established 1732, very friendly and qualified service, and of course you get complimentary espresso to neutralize your sensory apparatus after trying a flight of fragrances.
There's also a Douglass (the perfume chain monopolizer) flagship store on the main shopping street Zeil. While I believe in supporting small privately owned stores this deserves mention insofar that they do carry a limited amount of Creeds, Acqua di Parma, Etro, Joe Malone and loads of other designer stuff. Good for reckless indulgence in self-testing, generally rather unqualified staff.