There are a few things from org.eclipse.ui.* that haven't been ported to e4, including opening a preference dialog. I've attached a simple handler I use within Kizby to open a basic preferences dialog. This dialog doesn't include the search filter that's seen in the Eclipse UI as that's also under org.eclipse.ui.*. You'll also need to copy out org.eclipse.ui.preferences.ScopedPreferenceStore.
To use it, create a handler and bind it to your preferences command. Ideally you should continue to use the Eclipse 3.x command IDs when possible ("org.eclipse.ui.window.preferences") as it will be automatically wired up by platform-specific mapping code (e.g., org.eclipse.e4.ui.workbench.renderers.swt.cocoa will automatically bind the command to the "⌘-," keybinding on MacOS X).