My 2000 suby legacy outback sus 2.5 has what sounds like a transmission whine to it. It happens after getting to about 25 mph and only when accelerating, not while coasting. Any suggestions?

5 speed or auto ? have you checked front diff oil level ?   If its an automatic  try some additive (sea foam , lucas...) see if it helps . If its a five speed live with it but keep your eyes open for another tranny.  Japanese take out trannys are available although pull and save would be cheaper. 

How are your tires? Are they all matching? I know my five speed did this when I put a used set of tires on that had slightly different tread wear, they were a matching set, but the fronts had a little more tread than the back.

Bad pinion (auto or manual) may sound like this: