Hyperdesk for Vista should be coming out very soon. We're more than halfway done porting the themes over to Vista. Just finishing up the icon codes and some app crapp.
Both have their charms. Really you just shoot for the theme you like since both are basically theme distribution apps. To address some comments...
You can pick and choose which elements to install for Hyperdesk. So if you want to apply the hypertheme but not the icon set then you uncheck the icon button. Most of the themes have multiple icon sets so you can take it further and select an icon or theme substyle or set and then apply.
Lightstar: Yes its a known issue when you switch to small icons. When you go back to large they come back. Dunno why. You can always just pin the apps to the start menu and change them manually.
Hyperdesk does not have transparency. Vista version will have it where Vista allows it.
We do have the official themes for Star Trek, Disney and WALL-E which I'd be more than happy to port into Master Skins if someone from Stardock gave us the okay and wanted to discuss it... cough cough.