Prefs in moderation
Every additional selection in your application means additional complexity for the user. Before writing any preference controls for your application, consider these two warnings:
Make sure that a preferences item adds real value in the eyes of the user.
Don't add a preferences item just because you couldn't reach a decision. It's very easy to settle a dispute about how something should work by adding yet another preferences item.
Don't add a preferences item just because it's technically feasible to do it. Make sure it adds real value in the eyes of the user. (Note: we speak from experience here. Trust us on this one.)
The 90% Rule
If 90% of your users prefer A, and all but the most obstinate of those who prefer B could live with A, don't bother making it a preferences item. Remember, it is far easier to add a control next version than it is to take one away.