Of course, the idea of an ancient, malevolent alien race is nothing new, but the specific story of a group of aliens with unknowable motives invading the galaxy every few thousand years to wipe out all technologically-advanced species (while leaving the rest alone, unless they happen to be unlucky enough to share a planet with one of those advanced species) is something I've only seen twice; once with Freespace and once with Mass Effect.
Considering the additional similarities between the Ancients and the Protheans, and between Aken Bosch and the Illusive Man, and also considering the fact that the Freespace games were published by Interplay in 1998 and 1999 (the same time period in which Bioware was publishing the Baldur's Gate games through Interplay) and it seems pretty clear that Bioware was cribbing off of Volition's notes.
And, of course, when Bioware ran out of source material with Mass Effect 3 they made a complete mess of things.