Here's the "original" audio system in my daily driver: a '99 Accord LX 4Dr. It was as configured here for almost 7 years before I decided to upgrade. There is still alot to be said about an beautifully simple system config. I still believe the old system was quite awesome in its own right.....

My goals then were simple, and were reflected in the system design:
1) Keep it simple. Keep component/equipment count as low as possible, and do not do anything to degrade signal quality within reason.
2) Keep it functional: need room for golf clubs, two kid's car seats, etc.. Don't mess with the utility of the car as it is used.
3) Stealth look to ward off potential thieves.
4) Best sound for driver in particular, and reasonable dynamic range & SPL.

System component list:
- Alpine CDA-7940
- Phoenix Gold XS6600 Amplifier
- Dynaudio System 220MKII Component Speaker Set
- (2) Boston Acoustics Pro Series 12.5LF Subwoofers (in 2.0ft^3 sealed)
- Stinger 1.0 farad monitor capacitor
- Associated wiring, circuit breaker, etc...

Notes:
- The sub box allows free access to the spare tire without removal. It can also be removed very easily if needed.
- The sub enclosure is all 3/4 MDF, and perfectly fits the back seat and trunk contours. Only two sides of the enclosure are parallel. The drivers fire through the rear seat, and the enclosure seals pretty well with the back seat opening.
- No processing, time alignment or other methods are utilized in the system.
- No sound deadening was added to the vehicle.

edit: note my new system does utilize a full DSP, with time alignment and all active crossovers. Sound deadening is also utilized extensively, and the overall sound is better. But it sure did require alot of hard and SMART work.