Hello,
1999 Audi A4 B5 Quattro manual 5 speed making a knocking sound coming from Transmission ONLY on acceleration. I hear it in all gears except 1st. The faster I accelerate the louder it gets. It sounds like I have a playing card stuck in my bicycle spokes. I have replaced the fluid, the driveshaft and removed the Torsen differential and replaced the bearings in it. I put the car on a lift and with it running in gear the noise sounds like it is coming from the tail of the transmission yet the new bearings in the Torsen differential didn't help.
The noise stops the moment I let off the accelerator and starts as soon as I accelerate again. At all speeds 5-100 mph.

 

I have the same sound in my 5 speed, but only in first. Was pulling away from a stop sign with my foot on the floor (just where it should be) and it wasn't in gear all the way. Popped out with a huge sound, and now I sound like I've got a baseball card in my spokes when I'm in 1st.

That was about 20,000 miles ago, and the sound is no worse than the day I did it. Indy Audi tech I know said he's seen those go for years with no ill affects...except the sound.

However, I'd be surprised if I drive 5 miles a year in first gear. Not sure I'd be so nochalant about your problem.

 

Something is obviously fucked up inside the transmission.

If you think it wont break down, keep on driving.