There are a variety of afflictions that can be found on tree fruits, from fungal rots to bacterial infections. There are a number of options for dealing with these, and it all starts with rootstock and varietal selection. Choosing varieties suited to your climate, and rootstocks that have been bred to be resistant to the diseases and pests most likely to affect you, is the first line of defense.
Knowing which diseases and pests are likely to affect your trees is paramount. The Tree Fruit Field Guide is a very handy reference to carry with you into the orchard, and it's now available online as a searchable database.
You can also find some very helpful information on the identification and management of fruit diseases at the website for the Penn State Extension program and, of course, there is a wealth of other information in our Resources and Links page.