I got Bose in my '03, but only because the previous owner had it installed - I wouldn't pay for the difference. I also got HK in my M3, but only because the base system was such complete crap. In general, however, I think there are VERY FEW factory upgrades that are worthwhile - Infinity and Lexus probably being the exceptions. On a 1-10 scale, I would rate the 996 Bose (and I have the '03 MOST system) a 6.

 

For my .02

I spend more time feeling out the gas pedal to make the rear end sing rather than listening to quality of the music. I have the HIFI but its a pretty standard car radio sound, yet I couldn't care less. I also like the look of the OEM radio in the console because I love the stock look, wihtout the aftermarket.

 

I went down the high end route with a previous car and never thought it was worthwhile. My 02 has the Bose system and it's ok. The stereo upgrade money on this car has gone into the suspension.

 

I have Bose in both my Benz and my C4S. Both are very similar with maybe a slight edge to the P-car. It's nice to have an OEM sound system as opposed to dealing with aftermarket solutions. But here in TO when rush hour traffic is at a standstill, is when I really listen to music at a higher level. Other than that I use it for news and as background music at a fairly low level; you still need to hear the engine (PSE!) and what else is going around while driving in this congested city.
Bose sounds best when the engine is off and you're detailing the interior. Might also help at resale a bit.