Not a big sample for high mileage, but the evidence points to these engines being bullet proof. Look at all of the heavily modded, regularly tracked, boosted engines. I can't point to a single "common" issue (or any issue for that matter). That is pretty phenomenal.
Compare this to the 335i, which have a gazillion common issues; bad fuel injectors, high pressure fuel pumps, spark plugs, carbon build up, over heating, rare turbo failures, over heating due to inadequate oil cooling, etc. The N54 motor seems pretty bullet proof, but the peripherals, Turbos withstanding, aren't anywhere near the M3's caliber.
The common quality complaints on the M3 are mostly limited to "superficial" issues, like body panel gaps not being perfect, squeaks and rattles, and the notorious "cow bell." I experience the cowbell when my car had 70 miles on it and started freaking out until I realized I just needed to get a rock or whatever from behind my brake rotor heat shield.