For the most part, the last car system I heard that sounded any good at all was a circa 1975 Nakamichi a/d/s biamped Mobile Fidelity System.
I have heard many after market systems most of which were pretty bad but I am with Cruz123 - most stock systems, especially the upgraded ones are TERRIBLE.
Albertporter, I am shocked. I heard the BMW system in a new M5 earlier this year and thought it as TERRIBLE. Maybe the one you heard was significantly different.
Bose systems? Forget it. TERRIBLE.
And "Mark Levinson" systems? TERRIBLE. No relation to the real Mark Levinson whatsoever.
I have noted only one exception as mentioned by Audiojedi:
Although I bought the car for the interior and the performance, I have been pleasantly surprised with the system in our '07 Volvo V70 R wagon.
It is not boomy or bloated at all, the flat settings on the tone controls sound surprisingly neutral, and in general it is remarkably smooth and fatigue free for a car system. Yes, I believe the speakers are made by Dynaudio.
Have not heard the B&O system or the megabuck Naim systems, but maybe they are good.
Not sure if the stereo was the same, but the substantially similar Volvo R wagon has been made since 2004 so you could search around for a bargain. Practical, nice interior and can easily be tuned to 400 HP.