It was in use at least up until the middle of last year, principally for flying out newly-built Hawks to Warton, until production was run down.
It was only used for that purpose most recently, they had been roading them out for years before. I tend to believe that the reason they reopened the runway for delivery flights was in part to cover up the managed decline of the factory production. Hawk production is to move to Salmesbury, the factory will be closed in the next few years.
Prior to 2008, the runway had not really been used since the Warton J31 shuttle flights ended in 1992. I think Humberside Police Flying Club had a C150 based there for some time (since moved elsewhere), and the Blackburn B2 used to be based in one of the hangars making the occasional flight.
The nail in the coffin for Brough was the building of a chimney at Cappa Pass on the approach in the late 60's. The airfield instantly lost its licence for civillian flights, Autair went elsewhere and the runway was never extended past its short 3400ft. I think Hawker Siddeley were the only tennants happy to allow civillian movements at Brough anyway, and BAe didnt tend to like the idea of any resident flying club being on site in later years.
BAe Systems claim that if any new tennant of the site need to use the runway (some unnamed interested parties have been interested in the airfield as part of the package) then the runway will be retained and the site not built on. I find that hard to believe though, and East Riding Council didn't help matters by granting outline planning permission to build a retail park and link road on the runway.
A shame really, as anyone who knows the area will know how accessible the site is may agree that had the local councils not lacked vision decades ago, Brough would have made an excellent airport for Hull.