Ugh, there was just another thread about this very same thing not even a week ago.
Its the gears and bearings making noise. When you let the clutch out the gears and input shaft are spinning at the idle speed. If you rev the car up it probably dissipates and then when back down at idle you can hear it like its a lumpy clunking sound. Thats normal for the b13/b14 trans when they get up into age. Usually just caused by worn input shaft bearings. Again nothing to really worry about, its not going to grenade on you or anything. Best to probably change the oil and maybe go with at thicker gear oil to help ease the noise some, You could do a mix of Mobil1 75w90 and Valvoline 85w140, maybe half and half and that should help the noise.
You can either replace the trans if its too annoying but more than likely if the new one you get has any age to it, its probably gonna do the same thing. Or tear the trans apart and have the bearings replaced on the input shaft, mainshaft, and diff. Might as well do all of them if your going to tear into it.