I used to be HUGE into car audio. I had a system in a previous VW Jetta that was probably worth more than the car.
However, stock audio systems have improved by leaps and bounds so there is really no need to go crazy with car audio anymore. Just a few upgrades can make a stock system sound really top notch.
The only upgrade I mad to my Shaker 500 is to change out the speakers in the front and rear doors (not the subs though). I always thought the stock speakers sounded a bit harsh on some music material when played at louder volumns.
So I replaced the stockers with 4 Infinity Speakers. The Infinity's sound much smoother without sacrificing that nice high frequency detail that I like. So replacing those speakers with any good aftermarket speaker will give you noticeable improvement.
The only other upgrade I was thinking of is a powered subwoofer in the trunk. Since I have a convertible, bass response really falls off with the top down. A powered sub would help that immensely.
2007 GT convertible - black 5 speed MT: charcoal aluminum panel, black/dove int, anti-theft, cloth top, GT appearance pkg, MODS - MGW shifter, CDC Conv Light Bar, Pony 12V plug, Shelby Hood Pins, Steeda Strut Tower Brace, Steeda Strut Tower Covers, FRPP GTA's, CDC Classic chin spoiler, GT500 spoiler, Agent47 Mirrors, 18" Chrome DD bullitt rims/Continental tires, C&L CAI, Infinity speakers, RoadWire 2-tone leather interior, 4.6 badges, Dyno Tune-Mongillo Motors-New Haven-CT-301 rwhp/297 rwt