There are a few FM in Vienna, but usually only on Friday and Saturday in the area of the regular markets (Naschmarkt, Brunnenmarkt, Karmelitermarkt, Kutschkermarkt, Rochusmarkt, etc.).
The largest FM are Saturday morning:
1. between Naschmarkt and the flea market south of Naschmarkt.
2. at Brunnenmarkt
3. at Victor Adlermarkt.
Here is a link of all FM in Vienna: http://www.wien.gv.at/ma59/mpb/lapp.htm