The Washington Post had a piece this week that was based on visualization done by Seth Kadish about the 20 longest non-stop flights in operation today.
The longest running flight for reasonably long time was the all business class Singapore Airlines one from Newark to Singapore that according to the Great Circle Mapper was 9,534 miles.
You can access the Washington Post article here.
I just took Abu Dhabi to Sao Paulo the other day that is bit shorter than the Dubai to Sao Paulo Emirates flight that is on this list.
Many of the ultra long-haul flights became unprofitable when the price of the oil spiked that lead to cancellations of the Singapore Airlines and Thai Airways direct flights from the US to their respective hubs.