There are examples of elliptic fiber spaces over a two-dimensional base which have infinitely many relative minimal models (where two abstractly isomorphic models connected by flops are counted separately). The one I know is given by Reid and Kawamata and works by repeatedly flopping two rational curves in a singular fiber. In Matsuki's "Introduction to the Mori Program" he indicates (pg. 366) that this construction can be extended to a non-relative setting to yield a variety $X$ with infinitely many minimal models over Spec k.

I haven't managed to make this extension or find it written down, so a couple questions: where can I find an explicit example of a variety with infinitely many minimal models (over Spec k)? What is the Kodaira dimension in this case? Is it possible to find a Calabi-Yau threefold with infinitely many minimal models?

markedminimal models, which introduces even more non-uniqueness into the picture! – user5117 Sep 15 '11 at 13:56