How was this subfloor cleaned?
What kind of flooring are you putting down? If it's tile, I'd probably reinforce the floor a bit first with a new layer of t&amp;g subfloor before putting the tile down... which solves your problem. 

If there's any musty smell, you can clean the floor with trisodium phosphate (the real stuff, not "substitute") ... but don't soak it. Just scrub it with the tsp and a scrub brush. The TSP will probably take up the glue as well... but has a significant chance of eating your plywood in the process. ;)