diff --git a/src/main/java/org/scijava/module/DefaultModuleService.java b/src/main/java/org/scijava/module/DefaultModuleService.java
@@ -54,6 +54,7 @@
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.plugin.PluginService;
import org.scijava.service.AbstractService;
import org.scijava.service.Service;
import org.scijava.thread.ThreadService;
@@ -87,6 +88,9 @@ public class DefaultModuleService extends AbstractService implements
	@Parameter
	private ThreadService threadService;

	/** Index of registered modules. */
	private ModuleIndex moduleIndex;

@@ -255,6 +259,54 @@ public <T> ModuleItem<T> getSingleOutput(final Module module,
		return getSingleItem(module, type, module.getInfo().outputs());
	}

	// -- Service methods --

	@Override
@@ -383,5 +435,4 @@ private <T> ModuleItem<T> getSingleItem(final Module module,
		}
		return result;
	}
-
}
diff --git a/src/main/java/org/scijava/module/ModuleItem.java b/src/main/java/org/scijava/module/ModuleItem.java
@@ -93,13 +93,21 @@ public interface ModuleItem<T> extends BasicDetails {
	 * Note that this is different than obtaining a module instance's current
	 * value for the input; see {@link #getValue(Module)} for that.
	 * </p>
	 */
	T loadValue();

	/**
	 * Saves the given value to persistent storage. This allows later restoration
	 * of the value via {@link #loadValue()}, even from a different JVM.
	 */
	void saveValue(T value);

	/** Gets the function that is called to initialize the item's value. */

diff --git a/src/main/java/org/scijava/module/ModuleService.java b/src/main/java/org/scijava/module/ModuleService.java
@@ -42,6 +42,7 @@
import org.scijava.module.process.ModulePreprocessor;
import org.scijava.module.process.PostprocessorPlugin;
import org.scijava.module.process.PreprocessorPlugin;
import org.scijava.service.SciJavaService;

/**
@@ -273,4 +274,15 @@ <M extends Module> Future<M> run(M module,
	 */
	<T> ModuleItem<T> getSingleOutput(Module module, Class<T> type);

}
diff --git a/src/main/java/org/scijava/module/process/SaveInputsPreprocessor.java b/src/main/java/org/scijava/module/process/SaveInputsPreprocessor.java
@@ -34,6 +34,8 @@
import org.scijava.Priority;
import org.scijava.module.Module;
import org.scijava.module.ModuleItem;
import org.scijava.plugin.Plugin;

/**
@@ -51,6 +53,9 @@
	priority = Priority.VERY_LOW_PRIORITY - 1)
public class SaveInputsPreprocessor extends AbstractPreprocessorPlugin {

	// -- ModuleProcessor methods --

	@Override
@@ -66,7 +71,7 @@ public void process(final Module module) {
	/** Saves the value of the given module item to persistent storage. */
	private <T> void saveValue(final Module module, final ModuleItem<T> item) {
		final T value = item.getValue(module);
-		item.saveValue(value);
	}

}
diff --git a/src/main/java/org/scijava/options/OptionsPlugin.java b/src/main/java/org/scijava/options/OptionsPlugin.java
@@ -34,10 +34,11 @@
import org.scijava.command.DynamicCommand;
import org.scijava.event.EventService;
import org.scijava.module.ModuleItem;
import org.scijava.options.event.OptionsEvent;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.SingletonPlugin;
-import org.scijava.util.Prefs;

// TODO - outline for how to address issues with options (initializing, aggregating into 1 dialog)

@@ -77,6 +78,12 @@ public class OptionsPlugin extends DynamicCommand implements SingletonPlugin {
	@Parameter
	protected EventService eventService;

	// -- OptionsPlugin methods --

	/** Loads option values from persistent storage. */
@@ -95,7 +102,7 @@ public void save() {

	/** Clears option values from persistent storage. */
	public void reset() {
-		Prefs.clear(getClass());
	}

	// -- Runnable methods --
@@ -116,13 +123,13 @@ public void run() {
	// -- Helper methods --

	private <T> void loadInput(final ModuleItem<T> input) {
-		final T value = input.loadValue();
		if (value != null) input.setValue(this, value);
	}

	private <T> void saveInput(final ModuleItem<T> input) {
		final T value = input.getValue(this);
-		input.saveValue(value);
	}

}
diff --git a/src/main/java/org/scijava/prefs/AbstractPrefService.java b/src/main/java/org/scijava/prefs/AbstractPrefService.java
@@ -0,0 +1,53 @@