Howdy,
I've used ObjectDock Plus and RightClick to replace the entire Windows interface; taskbar, systray, everything.

The only issue I've had with ObjectDock's systray so far is that the tooltip of certain applications don't update the same way they do on the standard systray. I've written an application that demonstrates this, it's a simple wallpaper cycler that shows the time to the next cycle when you hover over the systray icon. It's a C# 2005 application and the mousemove event isn't raised unless the icon is actually clicked. Otherwise it's working as expected, but it would be nice if this could be fixed.
I'd also love to see an option for "expansion direction" so that if I have a dock on the bottom of the screen, set all the way to the left, the expansion only happens to the right. I have two docks on the bottom of my screen, one with the start menu docklet and the taskbar, the other with the systray. I'd like to be able to tell the taskbar dock to expand only to the right, and the systray dock to expand only to the left.