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Originally Posted by Sage
ShapeShifter will only cause a minor slowdown when launching apps (since that's when it's "telling" the application to look for GUI resources elsewhere), but it's very minor (less than a second), and it doesn't affect performance at all while you're using the application, just launching. I don't know about other Haxies, although I know ClearDock won't such up any power either.
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I disagree. Shapeshifter slows the Finder and iChat down on my dual 1.42ghz G4. Perhaps it slows down Cocoa applications? I recently updated to 10.4.2 and was amazed at the speed of the Finder. I then re-themed the GUI with Shapeshifter and things promptly became slower. Window resizing, scrolling, moving...the list goes on.
If you would be willing, I recommend you do an aqua-restore and log out and then back in. Things may be twice as snappy for you.
That said, fixing Apple's mess of a GUI via Shapeshifter is worth the relatively minor speed hit.