Having considered both when ordering my (E90) M3, I opted for the M3. I'm torn on the exterior styling of the 1M, didn't care much for the quality of the "Boston" leather, and didn't like the fact that it has no sunroof. What caused me to even consider the 1M was the value quotient (comparable performance to the M3 for less money), relative exclusivity, and that Valencia Orange paint option.
Both are superb cars IMO; you have to decide what it is about each vehicle that will cause you to make your ultimate decision.
2011 E90 M3 Alpine White on Fox Red
2007 E90 335I Graphite on Terra
2005 E83 3.0I Mocha on Black (Gone and forgotten)