It depends on what features you need. If you must minimize to the tray, it'll be easier in WPF. Silverlight, however, supports notification toast for notifications. It's not trayed, but it still works well.
Also note that Silverlight doesn't have floating child windows, so if you need them, you'll need to go WPF. You can get close analogs with the ChildWindow control, but they must stay within the bounds of the Silverlight application as they are ui elements, not real hwnd windows.
Silverlight 4 lets you do almost anything you need using COM automation. However, resist using that for major functionality. If you're targeting just Windows, do a click-once WPF application, preferably WPF4 if your timeline permits it. Reserve COM automation for OS "light-up" functionality in otherwise cross-platform applications.