The 2011 mini has a Thunderbolt connector, four USB2 ports, and a FW800.
Because Thunderbolt is so up-and-coming, the temptation is to go with that for the purpose of future usability. However, Thunderbolt eternal drives remain prohibitively expensive on a per GB value basis. For example, the WD MyBook 4TB with Thunderbolt, is $550 when you include the $50 cable.
FW800 used to be my go-to connector when I was editing a lot of video and it was the standard in that industry. But those days are slipping behind us quickly.
Finally, USB2 is the slowest connector there, but it has the virtue of bing able to connect USB3 external drives, which are much cheaper than Thunderbolt drives. Because the new MacBook Pros and Airs support USB3 in addition to Thunderbolt, it's reasonable to assume that future minis will support USB3.
Therefore, for the next year or so, USB3 would seem to me to be the best solution for your external storage needs. You will be able to use the drive case with your next Mac or PC, and it's backward compatible with USB2.
Here's what i would purchase:
http://www.amazon.com/gp/product/B004VFJ9MK
http://www.amazon.com/gp/product/B003UI62AG
Good luck, and let us know how it works out for you!