There are, at least, three CHEAP airline companies that go to/from the airport of Girona:

RyanAir flies very cheap from various european cities: Paris, Turin, Brussels, Frankfurt, Karlsruhe, ...

Transavia, an airline from Holland, flies from/to Rotterdam.

JetairFly, an airline from Belgium, flies from/to Brussels, Köln ...

There is a bus connection, provided by SARFA, to/from Girona airport to Empuriabrava. Here is the timetable for 2008:

There is also a mini-van taxi that goes to/from Empuriabrava to/from Girona airport for about 20 €. It has to be reserved, and you can do it in their web page or by phoning them.