Someone brought this up last week, there is a TSB on it and BMW will replace your clutch free of charge. Do an archive search, it was brought up not long ago, the full TSB is posted in the thread.
Edit: I looked it up myself:
Here it the clutch TSB:
As per SIB 21-01-01:
A popping sound or clicking sound may be heard from the clutch pedal at the last third of the clutch pedal travel when the clutch pedal is engaged or released
Procedure: Only if the customer complains of the above symptoms should the clutch be replaced.
Affected vehicles:
All E46's produced up to 3/01 (M52TU, M54 and S54 engines)
All E39's with 6 cylinder engines made from 9/97 to 3/01
All E39's with 8 cylinder engines from 9/96 to 3/01
All X5's with the M54 engine up to 3/01
All Z3's from 9/98 to 3/01
All Z8's up to 3/01
Edit: I looked it up myself:
Here it the clutch TSB:
As per SIB 21-01-01:
A popping sound or clicking sound may be heard from the clutch pedal at the last third of the clutch pedal travel when the clutch pedal is engaged or released
Procedure: Only if the customer complains of the above symptoms should the clutch be replaced.
Affected vehicles:
All E46's produced up to 3/01 (M52TU, M54 and S54 engines)
All E39's with 6 cylinder engines made from 9/97 to 3/01
All E39's with 8 cylinder engines from 9/96 to 3/01
All X5's with the M54 engine up to 3/01
All Z3's from 9/98 to 3/01
All Z8's up to 3/01