Most non-equipment related problems in car audio are the result of poorly chosen ground points. Always check the integrity of every connection including the battery, head unit, amplifiers and signal processors. Any part of the audio system can bring noise into the system. In general your connections need to be secure (grounds should be to the chassis), the charging system should be in top condition and all factory connections (battery posts, ground strap, alternator connections) should be secure. You may need to increase the size of your factory ground if you install a very large stereo system. It should also be noted that the negative battery post is usually a terrible place to ground car audio equipment. All of the ripple (noise) from the alternator and other items in the vehicle travel to this point. If you choose it as a ground point then you are inviting all of these elements into your sound system.
Alternator whine is the granddaddy of car stereo noise. The most common and the most annoying. Alternator whine will be heard as a high pitched whine that will rise and fall with the engine speed. Most of the time this is caused by a poorly chosen ground for a piece of equipment. It is usually cured by grounding the equipment directly to bare metal on the chassis rather than an available factory ground bolt as is often used to save time. You'll also need to make sure your charging system is in top condition and that your connections between the battery and components are secure as well as the integrity of the factory ground strap, an often overlooked component. You might also consider switching your RCA cables to a twisted pair model. Twisted pair cables will usually be less prone to noise than their coaxial counterparts.
Accessory pop is associated with one particular electrical event in the vehicle. This can be switching on your turn signal, headlights, brakes, windshield wipers or even the rear window defrost. These high current drawing accessories are causing a voltage spike that is traveling into your car audio equipment with the result being heard as a sharp pop. Adding a small bi-polar capacitor (0.47 uF) between the accessory's power wire and ground will often absorb these surges. You may need to place the capacitor on the load or the power side of the switch (maybe both). See the diagram below to see how this is done. Note that the diagram is slightly different if the accessory has a relay in the circuit.