I believe the Cybermen would, in the time when they first on tv, likely have been seen as allegories for totalitarian communism (or at least the Western perception of it).
The Zygons as portrayed in the 2015 episodes 'The Zygon Invasion' and 'The Zygon Inversion' are clearly inspired by modern-day Muslims - we see them living in the UK as immigrants and refugees, with some of them happily integrated, others simply keeping to themselves, and yet others forming an obvious Daesh analogue, complete with a similar flag and execution videos. UNIT even targets Zygon extremists with drone strikes, in a vague Middle Eastern country for good measure. This is all a new development, however, and not (as far as I know) reflective of the Zygons of classic Who.