Yes, there are still referenda in the European Union that are not EU-related:
In Latvia, a referendum that aimed at giving the population the right to dissolve the parliament has failed due to low turnout (39% instead of >50%).
But since 97% voted in favour of the constitutional amendment, Latvian president Valdis Zatlers (who is without particular political power) has proposed to the parliament to amend the constitution by itself.
Latvia would be the first European country to give its population such a right.
Read also on this topic (updated):
Elia Varela Serra