I get this too, although I wouldn't call it knocking. More like a scraping sound - it usually happens in second, sometimes in first. Sort of an intermittent, dragging sound. If I had to guess it would be that a bearing in the transmission is going out - is that possible? It sounds like its coming from the left side of the car.
I dropped the tranny a few months ago and put in a new flywheel and clutch - had no effect on this sound, which has been present for awhile now.