Use a SettingsManager class or something similar that is used to abstract getting all settings data. At each point in the code where you need a setting you query the SettingsManager class - something like:
int timeout = SettingsManager.GetSetting("TimeoutSetting");
You then delegate all of the logic for how settings are fetched to this single manager class, whose implementation you can change / optimize as needed. For instance, you could implement the SettingsManager to fetch settings from a config file, or a database, or some other data store, periodically refresh the settings, handle caching of settings that are expensive to retrieve, etc. The code using the settings remains blissfully unaware of all of these implementaton decisions.
For maximum flexibility you can use an interface instead of an actual class, and have different setting managers implement the interface: you can swap them in and out as needed at some central point without having to change the underlying code at all.
In .NET there is a fairly rich set of existing configuration classes (in the System.Configuration) namespace that provide this sort of thing, and it works out quite well.
I'm not sure of the Java equivalent, but it's a good pattern.