I'm not sure whether this is non-trivial or not, but do there exist simple examples of an affine scheme $X$ having an open affine subscheme $U$ which is not principal in $X$? By a principal open of $X = \mathrm{Spec} \ A$, I mean anything of the form $D(f) = \{\mathfrak p \in \mathrm{Spec} \ A : f \notin \mathfrak p\}$, where $f$ is an element of $A$. 
Let X be an elliptic curve with the identity element O removed. Let U=X-P where P is a point of infinite order. Then U is affine by a Riemann-Roch argument. Now suppose that U=D(f). Then on the entire elliptic curve, the divisor of f must be supported at P and O only. This implies that P is a torsion point, a contradiction. 