This is a tough choice. I guess it really comes down to your personal situation. If you have a family and it will be your only car, then the M3 would be the ideal choice. If you are single or have another car, then the 997 would be the ideal choice. For the record, there are amazing deals on pre-owned Porsche 997's (and most have VERY low mileage).
I'm just hoping that my wife won't get too upset with me if I trade in my 330i and pick up both of these cars in the next year or so.
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2008 BMW 535i Space Gray, Black Leather, Dark Bamboo Trim| Sport Automatic with Paddles | Sport Package
2008 BMW M5 (gone, but not forgotten) Space Gray, Silverstone Merino Leather, Madeira Walnut Wood Trim | 7speed SMG | All options
Mods: Corsa Exhaust | RPI Ram Air Intake | H&R Sport Springs | Rogue Engineering 12mm spacers