Set theory
Set theory (which is expressed in a countable language), if it is consistent, has a countable model; this is known as Skolem's paradox, since there are sentences in set theory which postulate the existence of uncountable sets and yet these sentences are true in our countable model. Particularly the proof of the independence of the continuum hypothesis requires considering sets in models which appear to be uncountable when viewed from "within" the model, but are countable to someone "outside" the model.