Let $E = DTIME(2^{O(n)})$ and $NE = NTIME(2^{O(n)})$ be the deterministic/nondeterministic complexity classes of problems decidable in exponential time with linear exponent.
There are many examples of problems "underneath" this class, in $P$ and $NP$, and there are many examples of problems "above" this class, in $EXPTIME$ and $NEXPTIME$. But it seems nice examples of problems that belong to $E$ or $NE$ are scarce.
What are some nice (natural, non-artificial) examples of problems in these complexity classes?