I need a radio that is waterproof.  What are my options?

There are not any marine radios on the market that are fully waterproof.  The closest you will get are radios that are are water resistant.  Even these radios can be damaged if they subject to too much water or moisture.  Fortunately, most marine radios have the option of adding wired or wireless remotes.  This allows you to install the head unit in a location that is out of the way, and hopefully less likely to be subjected to excessive wetness or moisture, while still allowing you to easily operate the radio's functions.

Can I use regular car audio equipment in my boat?

Standard car audio equipment functions on 12 volts, the same system that is in your boat.  This means that you do have the option of installing car audio gear in your boat.  However, there are quite a few things to consider before you decide if this would be a wise decision for your paticular application.  First off, you need to determine how frequently your boat's stereo system will be subjected to the elements.  If you take your boat off the water after each use and always keep a cover on it, then standard car audio equipment might work just fine for you.  However, if you keep your boat docked all summer and only cover it when you winterize it, then you probably want to get marine gear that is going to withstand as much moisture and wetness as possible.

Keep in mind, its always best to have "more than you need" when it comes to protecting your audio equipment from the environment.  Even a single incedent of forgetting to put the cover on, or getting caught out on the lake in the middle of a rain storm can easily damage standard car audio equipment.

How can i better protect the stereo equipment in my boat so that it lasts longer?

There are multiple ways to accomplish this.  First, there are some fairly logical solutions.  Installing equipment out of the way (such as amplifiers and head units) in areas that protect them and make it less likely for them to get wet is a good idea.  Generally, up under the driver's console or near the front of the bow are good options for this.  If you must install your head unit in a less protected area, a marine cover will definitely help.  These clear plastic covers seal off the front of the radio, keeping water out.  They can be flipped up when needed, to insert a cd or operate the radio's controls.  Subwoofers can also usually be mounted in out of the way locations. 

Coaxial speakers however are a different story.  These speakers usually need to be mounted out in the open in order to produce good sound.  This leaves them subject to the highest likelyhood of exposure to moisture and wetness.  To make matters worse, your typical coaxial speaker often has a pole mounted tweeter.  This design has a small gap in the cone that can allow water to easily get to the speakers voice coil - the most delicate and easily damaged part of the speaker.  Because of thse factors, there is no good replacement for a true marine grade midrange speaker.  No non-marine coaxial speaker can ever be expected to last very long in the marine environment.

Would you recommend an amplifier for my boat speakers, or will the power from my head unit be sufficient?

The answer to this question really depends on what level of performance you are hoping to achieve with the audio system in your boat.  If you have a simple system on your pontoon boat, and plan on using it for background music while parked out on the lake, then running your speakers off of the small amplifier inside of your head unit would be more than sufficient.  If you don't plan on listening to your system very loud, and more important if you don't want to listen to the stereo while cruising at higher speeds, you don't need a ton of power.  A boat is very similar to driving with the top down on a convertible in the fact that above 25-30 miles an hour, wind noise starts becoming a major factor.  As speeds increase, the amount of output needed from a stereo to overcome the increasing ambient noises increases exponentially. 

With that information in mind, we can determine a few other things about the stereo in your boat.  If you plan on having good output from your stereo while at cruising speeds, a high powered amplifier with speakers to match is going to be a requirement.  How fast is the boat able to go?  How loud is the motor?  Do you want people being pulled behind the boat (on skis or a wakeboard) to be able to hear the stereo system?  These are all factors that need to be considered. 

Just like in the automotive environment, it is always better to have a little more power than you need than to find out later that you don't have enough.  We've never had a customer come back and say "I really wish I had put a smaller amplifier in my boat", but we have definitely had customers say the opposite.