An example of a Calabi-Yau 3-fold with irrational nef cone?  Let $X$ be a Calabi-yau 3-fold, that is, $X$ is a smooth projective 3-fold such that $K_X$ is trivial and $h^1(X, \mathcal{O}_X)=0$. 
Question Is it easy to find $X$ whose nef cone is not "rational", that is, 
the nef cone does not coincide with the convex hull of rational points on the nef boundary? 
 A: I think the following construction could work: Let $X$ be a Calabi-Yau threefold without any rational curves (such threefolds do exist). Then $Nef(X)=\overline{Eff}(X)$, i.e., the nef cone equals the pseudoeffecitve cone (by the log cone theorem) and the nef boundary is given by the null cone, that is, the set of divisor classes $D$ such that $D^3=0$. Note that this null cone is given by the zero locus of a degree 3 polynomial in the Neron Severi group, and the non-rational points of this will give you the example.
I should mention that the nef cone of a Calabi-Yau threefold is a very interesting object even though it is often non-rational polyhedral. Indeed, the Kawamata-Morrison cone conjecture states that the nef cone and movable cone should instead have a rational polyhedral fundamental domain for the action of $im(Aut(X)\to GL(N^1(X)))$. In some sense, this is the next best thing compared to the Fano case ($K<0$) where everything is rational polyhedral. So in particular if the automorphism group is infinite, then one would expect a non-rational polyhedral nef cone. 
