Careful pruning during the late winter dormant season is the best way to limit an established tree's growth. To prevent new growth on a cut stump, simply salt the trunk.
Probably the best way to limit a tree's growth is to start with a dwarf version of the appropriate tree. Dwarfs are genetically programmed to grow to a certain size and no larger. For established trees, however, the University of Virginia's cooperative extension program suggests pruning branches into the desired shape by clipping them off at approximately where they need to stop growing. Clean cuts just before the new growth season enables the tree to spend the shortest possible time with an open wound.
Another recommended method is containment. This involves using boxes or other containers to limit the root growth, thus limiting the tree's overall growth. However, using containment on a tree, while a good way to limit growth, decreases its quality of growth and the quality of any fruit it bears, ultimately shortening its overall lifespan.
If the problem is a stump that keeps sprouting fresh growth, drill holes into the top and sides and fill them with potassium nitrate. Any natural source of nitrogen, such as compost or manure, works as well. This technique kills the roots and encourages fungal growth, rotting the stump for easy removal as well as preventing new growth.