Lucie Miller once refered to Gordon as "Flash Gordon". (AUDIO: No More Lies)
Whilst in their spacesuits, Evelyn Smythe called the Doctor "Flash Gordon" and Thomas Brewster "Buck Rogers". (AUDIO: The Feast of Axos)
Behind the scenes
Crusty Cobbe, in COMIC: Rock Quasar and the Mudslugs of Gurrn, was named after Buster Crabbe who played Flash Gordon and Buck Rogers in serials in the 1930s and the 1940s.
The Lion-Men of Mongo were mentioned in Invasion of the Cat-People by the Seventh Doctor, who are also characters from the Flash Gordon franchise in the real world, though this is not made explicit in the DWU.