Have a look at the article I linked to in the first post. The effect on bandwidth will depend on the application and what you plug in. Raid cards, wifi, firewire/usb, PCIe sound cards etc should work at or near their full potential, as most of these cards only use a x1 link anyway. A graphics card may suffer from the reduced bandwidth, but my assumption is that even a crippled discrete graphics card will beat the onboard GMA950.
A perfect example is HDTV playback. The Apple TV uses a low-spec Intel chip but is still able to play back high quality HD signals because it uses the 7300Go gpu from NVidia. The gpu handles most of the HD decoding by itself. In our case, the Mini would be saved a lot of the processing. It would be able to play back HD content with no problems at all.
Another example is OpenGL support. It is my understand that the GMA950 has relatively poor OpenGL support. Ati cards, I understand, are much better in this department because they are able to process some of the OpenGL commands directly in hardware, instead of having the driver translate for them. This would free up the cpu and system ram for other things - sound, AI, etc.
Even if it turns out that a discrete GPU on a x1 PCIe link isn't as good as the onboard video (which I seriously doubt), we still have the potential to add far more peripherals to the mini then ever before. One could have a high-capacity server by using a RAID card and several disks, within the size of a shoebox! We could finally have Firewire 800, or turn the mini into a sweet little router with a 4xGbE card. I'm excited ^_^