Thanks for the input, Doug. I could probably use Parallel or Boot Camp for a short period, but I'm going to need a dedicated box sooner or later.
If I go with Sandy Bridge, do you have any recommendation on a particular mini-ATX board for it? I don't need WiFi, or much fancy...just want a solid board that I can put in something like the Antec Mini Skeleton.
I'm not a mini-ITX user. There are lots of experts on this board.
You might want to try booting a Live Linux via CD or USB on your Mac Mini and trying your app on that config. No repartition or install required. Use the relative performance and the type of Mac CPU you have to extrapolate your CPU performance needs for Linux. (Consider Knoppix 6.7 as an easy Live Linux for testing.) http://knopper.net/knoppix/knoppix67-en.html
(Assumes you can do this via EFI/boot camp. Have not verified.)
When you have determined your approximate CPU performance needs, use the search function on this site and narrow down your CPU choices. Consider checking sites like newegg.com to pick a few candidate motherboards. Be sure to read the reviews.
Also, goolgle for roundup articles like http://www.anandtech.com/show/4376/computex-2011-intels-thin-miniitx-sandy-bridge-platform
Resist the temptation to select something brand new, especially for Linux.
When you've narrowed down your choices to a couple of CPUs and a few motherboards, google the motherboard name and the word Linux to ensure that there are no issues with Linux compatibility, especially with videos.
Be aware that Intel's Linux video drivers are getting better, but still aren't high performance. If your app needs high performance video, consider adding Nvidia to your config.
Now that you've narrowed down your options, search again on this site to validate your choices. Finally, present you partially validated list of options to the members of this site for their expert opinions. The more work you do ahead of time, the better the members can help you. The more specifically you can define your preferred options, the better.