There are a number of ways to lower suspensions and what you use depends on the type and characteristics of the suspension on the particular model. Also, the total amount you want to lower the car can affect how you do it.
The method presented above by FujimiLover can be used on many metal axle vehicles. Most AMT kits in the 50's and 60's used this method, even supplying reversible axle blocks or two holes for the axles!
I simple leaf spring rear can sometimes be lowered slightly by simply filing down the mounting points at the ends of the springs. Another way is to add blocks of plastic above the springs to mount the rear end to. If the axle is suspended directly off coils. you can cut the coils down.
Independent front, or rear, suspensions can sometimes be lowered by moving the wheel mount higher up on the kingpin.
Cutting the coil-strut on a MacPherson type suspension can lower the car.
These are just a few methods to get you thinking about YOUR suspension. If you give the specific kit you're working on, I'm sure someone here has lowered it an can give some specific advice. One thing to keep in mind is maintaining wheel clearance to the body when lowering.