I also have an E46 BMW and a Boxster S. The two cars are very difficult to compare as they were built to serve different purposes. The E46 is my daily driver and performs masterfully, it is rocksolid and perfect for the daily grind of commuting to work, dropping off the kids, and traveling. The E46 also provides a smile with the torque of the inline-6 (I have the 2.5 liter 325i) and the incredibley smooth manual gearbox.
The Boxster S, on the other hand, is an entirely different car and experience. The Boxster is a raw open-top sports car (especially the 986) that stirs emotions I didn't know existed until driving the Boxster, with the top down through open country rodes and twisties. I've always been a "car guy" and I've owned several sports cars through the years and in my opinion none compare to the Boxster driving experience.
Just for fun here's a pic of my E46:
