If you were using Safari 3 beta and TransparentDock, and decided to uninstall Safari 3, you received a rude awaking when TransparentDock no longer worked as before. The reason is because Safari Beta 3 installs another version of Dock, and that version of the dock is incompatible with the current version of TransparentDock (which only works on PowerPC machines).
In order to get TransparaentDock working again, you have to restore the Dock from a back up and not use the current Dock. You may get a message telling you that your back up is not compatible with the current version of the OS. Go ahead and select it anyway and restart the Dock. After you restart the Dock, go ahead and apply the combo update to 10.4.9. This will bring your Dock back to its state prior to the Safari 3 beta install. After that, TransparentDock will work as before and you will be back in business.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20070615140501982