may want to look over these threads:
thinking-of-trading-in-for-06-m35-sport ... 83145.html
opinions-on-purchase-of-2006-m45-t580363.html
what-to-consider-with-a-used-m-t578253.html
But to summarize what I think I've seen/read:
1. A "rattle" under acceleration which is caused by micro cracks in the Y-pipe...you should take the car out and listen to it at idle, accelerating slow, hard, going into a turn, etc.
2. Some folks have had issues with the driver side seat rails breaking causing the seat to wiggle, rock, and move
3. There is a TSB for adjusting the Bluetooth microphone, poor sound/reception
4. The M has an issue with tramlining for some with certain brands of tires- lots of threads on tires
5. Oil consumption (I would want to see records of oil changes and regular maintenance items, especially if done at the dealer), more so with VK compared to VQ
6. Problems with filling up the gas tank only halfway before pump shuts off and obviously not completely filling up - this has happened to me about 2 times in about 4 yrs...I just pull the nozzle out, place in back and pump slow
7. Warped rotors from OEM setup, try Brakemotive kit, you won't be sorry
8. Wheel hubs going bad (just had to replace my front passenger after about >90k miles, though) pretty easy job - look at FAQ and DIY thread
9. If the CEL, VDS, RAS lights (basically if your dash looks like a Christmas tree) and you can't drive it or it's stuck in "limp" mode, the crank position sensor and/or camshaft sensor has gone bad and needs to be replaced (recent thread about that too)
Another thing to think about is bolt-on go fast parts, if you're thinking about modding: more aftermarket stuff for the M35 (VQ35DE) vs the M45 (VK45DE) but the M45 has more HP and torque stock, and only about 1 mpg less than the M35 (although Dean has demonstrated you can squeeze some great gas mileage out the '45 - very recent thread) !!!!
Good luck, you won't be sorry with either the M35 or M45.
If you pull the trigger, post pics of the ride and Welcome to NICO.
Craig