Using the rear as an example because it's simpler...
The shocks limit travel and absorb shock. I assume that the OEM springs and shocks are sized so that at full extension (for example, jack up the rear by the frame) there is just enough force exerted by the springs to keep them from falling out, but not so much that they overcome the damping of the shock and you get a harsh impact if it tops out.
If you put in longer springs with the stock shocks, then when the shocks top out the springs will exert more force on the shock, and you might feel the impact or damage the shock when it reaches the limit with more force than expected. You shouldn't top out very often with the stock configuration, but with a longer spring and stock shocks you might be near the limit of shock travel all the time, so it could happen frequently.
If you put longer shocks in and use the stock springs, the springs could fall out if the rear is unweighted since the shock could extend to the point where the spring is completely unloaded. You would probably have to get air or be on a surface that causes articulation for this to happen, but it could be really bad. If the springs fall out while you are in the air, when you land there will be no springs to support the weight and you could damage the shock or something else. I inadvertently hit a bump that turned into a bit of a jump in a 4runner one time, so it can happen. The springs didn't fall out because it was all stock. [MENTION=88975]Swarty[/MENTION] says the springs won't fall out, but I would want to verify that myself if I had different rear shocks. (jacking up the rear frame and checking the springs would be a simple test.)
The front is similar, but there are more parts that might limit travel if the shock/spring is changed from the original design. As far as I know the shock is the primary thing that keeps the wheel from falling down too far. Other things are the upper control arm joint, and the bushings on the control arms which do not move very freely when the alignment cam bolts are tight. There may be no sliding movement there, only the rubber bushing stretching. There's also the sway bar, which links the left and right sides, etc. The shock is designed to limit travel because if it breaks it's not catastrophic. If a control arm ball joint or something like that breaks while driving then you have a problem! A limit strap could work, too, but I've never seen a limit strap in an OEM suspension.
Adding a spring spacer or longer spring has the same effect as a longer spring in the rear, and you need a longer shock to compensate. A longer spring might be equivalent to a spring spacer because the minimum length of the stock spring + a spacer could be the same as the minimum length of a longer spring that has a lot of coils. Adjustable coilovers work the same way as spring spacers, but they are adjustable.
Adding a spacer above the top hat is different since it moves the spring and shock down together, but it doesn't change the relationship between the spring and the shock.
In the front and rear, rubber bump stops limit upward travel. They are not just a hard limit, but they actually make the spring force non-linear as you hit them so that you don't get harsh bottoming out on big bumps. If you add longer springs, spring spacers, or top hat spacers you might bottom out on something solid (metal) before you hit the bump stops, which could make for a harsh impact. If you add lift that limits compression you should probably add spacers to the bump stops, too, so that they can still absorb big hits.
Example of a top hat spacer:
Front Top Plate Spacer (One - 1/4")
Example of a spring spacer:
Front 2" Coil Spacer Lift for 00-06 Tundra
There's a lot to consider, and I still don't understand suspension well enough to change anything. We haven't even considered where the center of gravity is with relation to the roll center. The vehicle rotates around a virtual point called the roll center
https://en.wikipedia.org/wiki/Roll_center . And there might be effects on steering or handling if the suspension geometry is changed which might not be noticeable in normal driving. And there's also ride quality, which is difficult to describe accurately and difficult to compare or measure. Could someone test different suspension setups on a controlled course while recording accelerometer data for me? And there's the fact that manufacturers for all this stuff don't give us any parameters that we would need to design or compare suspension setups. For springs I want to know the uncompressed length, spring rate, and minimum (compressed) length. For shocks I want to know max an min length and how much compression damping and rebound it has, and if there are any special damping circuits such as high and low speed circuits (common in mountian bikes), and if the shock has any spring force of its own from a pressure charge. I also want that information for the stock springs and shocks to compare.
