Not counting Special member state territories what's the longest scheduled flight one can take starting and ending in an EU airport?
Air Berlin flight from Düsseldorf to Düsseldorf is a 12 hour sightseeing flight covering a distance of 9780 km.
Larnaca, Cyprus to Dublin, Ireland
Flight distance is 2316 miles (3727 km) and flight time of 5h 35m (via Cobalt Airseasonal route).
Cyprus is the easternmost country in the EU and this is the farthest flight available from it. If there was a scheduled flight to Lisbon it's be slightly better but not by much. Going from east-west is better than south-north due to going against the prevailing winds so it takes longer.
Helsinki to Lisbon on Finnair (Flight TAP Portugal 791) takes 4h55m and spans just over 3350 kilometers.
It's unlikely anything else could come close, unless there are charter flights from the northernmost Finnish airports.
Following up hippietrail's suggestion:
is 4420 miles, 7114 km, about 9 hr