Fantastic App, makes things a lot easier.
Some suggestions to make it better.
When you check for new themes how about check boxes for the ones you want to download.
A way of including the Browser.nib file with the theme, to allow for different sized icons than safari's 28x25 default (example the XP IE theme would look a bit 'squashed if the icons used the default size and position).
A simpler way to make up icon sets, how about draging .tif files from the finder and dropping them on the icons, like CandyBar does with icon files.