At this point in Apple's platform strategy, unless you're partial to PowerPC or have some love for resurrecting older Mac computers, I would highly recommend never purchasing anything from Apple without an Intel-based Core 2 Duo processor (or any subsequent processor release, as in the Xeon in the Mac Pros, etc.).
It is rumored (but not confirmed) that Apple will be dropping software support for the PowerPC platform in the near future. If this happens, that means that if you purchase a Mac mini with a PowerPC processor in it, bring it completely up-to-date with the latest version of OS X and applications, then that's as far as you're going to go with it.