I have a '99 540/6 with 110K miles and I think you are experiencing normal noise for that motor. I heard somewhere (probably on the Roadfly forum) that there was actually a TSB regarding the "rod knock" type of noise in the V8 and that it is normal. If you really listen closely, my car at idle, particularly with the A/C compressor on, sounds a little like an old WWII submarine under water, but once the revs go up the sweet music begins...
2006 Honda Odyssey EXL-RES
2006 Honda Accord V6 EX-L Sedan
1999 BMW 540i 6-Speed (Sold to M3UOND on 9/21/06)
1991 Honda Civic Si - Occasional Beater