You are replacing the entire stereo system in your car and don't really know where to begin. You know that you want it to be loud and clear, free of distortion, and get loud when you need it to.
Generally, you have two options.
1. Active system
2. Passive system
An active system is the most involved and requires a do-it-yourself approach. Basically you will be adding different speakers (subwoofers, woofers, mids, tweeters) and an amplifier channel to power each one separately. You'll need an active crossover to separate the signal before the amplifier.
A passive system will use speakers (usually a woofer and a tweeter) with a passive crossover that separates the signal after the amplifier.
A passive system will generally be simpler to set up and use fewer amplifier channels. An active system is easier to tweak/change components and if done well, will sound better.
If you want simplicity, then a good 6.5" component set and a 2 or 4 channel amp will give you good output. Add a 10" or 12" sub with a 200-400 watt mono amp on it and you will have a solid system. I personally like CDT audio for their speakers. They are a great value and really sound very good.
If you really want to get involved with your system, I would highly recommend that you learn more about active systems. They take more planning, but really aren't too difficult or expensive once you learn the ropes. Check out www.diymobileaudio.com for a gold mine of information on active systems.