The effective topos is an example of an elementary topos with a natural numbers object which is not a Grothendieck topos.
It is an environment for higher order recursion theory, where, in the internal logic, it is provable that every total function from natural numbers to natural numbers is recursive? (furthermore, the functor from the effective topos into Set preserves the natural numbers object, giving a suitable version of this result in the external logic as well).
It can be specified as the realizability topos for Kleene's first algebra.
The effective topos construction alluded in the above paragraph can be performed more generally, in every topos with a natural numbers object, replacing Set. To every such topos one constructs the corresponding “external” effective topos and the correspondence extends to a functor admitting a fully faithful right adjoint. Kleene’s first algebra can also be replaced by any partial combinatory algebra, or even some more general types of gadgets; toposes obtained in this way are called realizability toposes.
J.M.E. Hyland, ‘The effective topos’ in A.S. Troelstra (ed.) D. van Dalen (ed.) , The L.E.J. Brouwer Centenary Symposium, North-Holland (1982) pp. 165–216.
Sori Lee, Jaap van Oosten, Basic subtoposes of the effective topos, arxiv/1201.2571