Our startup built a plugin for Microsoft Outlook. It was successful, and customers wanted the same thing but for Outlook Express. Unfortunately, OE had no plugin architecture. But Windows has Windows hooks and DLL injection. So we were able to build a macro-like system that clicked here and dragged there and did what we needed it to. The only problem was that you could see all the actions happening on the screen. It worked perfectly, but the flickering looked awful.
At lunch, someone joked that we just had to convince OE users not to look at the screen while our product did its thing. We all laughed, then paused. We looked around at each other and said "no, that can't work."
That afternoon someone coded up a routine to screenshot the entire desktop, display the screenshot full-screen, do our GUI manipulations, wait for the event loop to drain so that we knew OE had updated, and then kill the full-screen overlay. Since the overlay was a screenshot of the screen, it shouldn't have been noticable.
It totally worked. The flickering was gone. We shipped the OE version with the overlay hiding the GUI updates. Users loved the product.