I too am having a similar problem, and reading this gives me some more insight. My warranty is up in 2 weeks (2008 M3) and I have only 17k miles on my car. I don't have as much of a squeal, but more so like a slighty humming or vibration/rumble when I come to a stop. Its only if I am at the point where I am at 20-15 mph as I come to a stop. I can't remember when it started doing this. Granted, the car stops perfectly fine, its just something that, not only is it heard, but it is felt, as well.
I have an appointment set for Tuesday and I am gonna telll them to check the entire car with a fine toothed comb and fix anything that needs to be fixed.
2008 (07/08) E92 M3 BPM Stage II Tuned by Mike Benvo, 6MT, Turner Test Pipes, Magnaflow Custom Catback Exhaust (Magnaflow X Pipe, secondary cat delete, Aero Resonators and Helmholtz Chambers),Vorsteiner CF Lip, Hamann Style CF rear diffuser, CF Rear Decklid Spoiler, BMW Performance Kidney Grills, CF Side Grills, OEM GTS Wheels, K&N Drop-In Filter, GP Thunder 8k Angel Eyes, Painted Reflectors.