I haven't personally tested both the Intel and AMD Mac Minis, but my experiences with integrated GPUs (such as the Intel HD Graphics 3000) have been less than impressive. Integrated GPUs are fine for people who primarily browse the Web, run productivity software, play a few non-graphics-intensive games, and don't work with or watch a lot of HD video. I don't fall into this category of user.
If you want to use the Mini as a small media PC (streaming HD video to a TV), do a lot of photo or video processing, or even play 3D games with an acceptable frame rate, I suggest going with the AMD version of the Mini.
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