Topos theory is a messy area with various rival factions and a problematic community. However we believe that Lawvere's original theory of elementary toposes and its subsequent development is important and interesting. The most important object in an elementary topos is the subobject classifier $\Omega$. If we think of the topos as a cell then $\Omega$ is a kind of nucleus. An elementary topos is simply a model of mathematics which as a foundation is vastly superior and more cogent than ZFC. To us the most important concept in topos theory is that of the Lawvere-Tierney "topology", which is just a morphism $j : \Omega \rightarrow \Omega$ satisfying three simple "modal" or "closure-operator" type axioms. A very important instance of $j$ is given by double-negation $\neg\neg : \Omega \rightarrow \Omega$, in which we consider the (internal) Heyting algebra structure on $\Omega$. The morphism $j$ then determines a localization of the topos, a new subtopos of the original topos called the topos of $j$-sheaves.
A central philosophical problem of topos theory is understanding the meaning of the Lawvere-Tierney "topology" and its associated topos of $j$-sheaves as well as the special role of the $\neg\neg$-topology (why is it not abuse to call $j$ in this case a "topology"?). A key to this is to see how the theory above abstracts the concrete case of presheaves and sheaves. A "sieve" is a curious concept. Think of a set $S$ of open sets (conceived as "cover") in some space $X$. Then take the minimal extension of $S'$ of $S$ under the condition that $U \in S$ and $V\subset U $ implies $V \in S $. Then we have a sieve (generated by $S$). We could rephrase the condition as $W \cap U \in S$ for any $U \in S$ and open set $W$. That is $S'$ is the $\wedge$-ideal generated by $S$. The we have the obvious notion of a principal idea generated by $O$ (called a principal sieve).
For the presheaf topos on a topological space $X$ we have that the presheaf $\Omega$ associates to each open set $U$ the set of all sieves on $U$. So $\Omega$ is a kind parametric version of local truth values. On the presheaf topos an important example of $j$ is the functor that associates to each sieve $S$ (on a $U$) the principal sieve determined by "what $S$ covers". In the words of Moerdijk and Maclane "What counts is what gets covered". Thus in this case $j$ is nothing more than a kind of parametric generalized union. Logically it is expressing "if something is locally true then it is globally true". That is the subjobject of $\Omega$ determined by $j$ consists in those sieves which are invariant under generalized union, situations in which if something is locally true then it is globally true. This fails for instance for the presheaf of constant functions. This $j$ (which we should call the union topology) seems to be intuitively clear but we still need to understand better why in the topos of continuous functions on topological space $X$ the internal logic of the topos proves that all functions are continuous.
Thus for the topos of presheaves on a topological space the subobject classifier on an open set $U$ yields all the sieves on $U$ while for the topos of sheaves it yields all the open sets of $U$ (or equivalently the set of principal sieves on $U$.
But a central problem of topos theory is understanding other $j$s such as the double-negation topology (and its "$j$-sheaves"), in particular as an abstraction of the topological sheaf case. We have written something about this in our "Hegel and Modern Topology". The double negation topology is all about "density" while the union topology is about local-global coherence. Could we associate the union topology with exponentials in linear logic ?
What does the double-negation topology look like for the presheaf topos on a category $C$ ? For the case of a topological space the subobject classifier of the double-negation sheaf topos on $U$ is given by the sieves $S$ on $U$ such that for every $V \subset U$ there is a $W \subset V$ such that $W \in S$. It is easy to think of sieves on $U$ which do not satisfy this condition which seems to be equivalent to saying that $\cup S$ is dense in $U$ in the classical sense.

