Are there Néron models for Abelian varieties over higher dimensional ($> 1$) base schemes $S$, let's say $S$ smooth, separated and of finite type over a field?
If not, under what additional conditions?
Are there Néron models for Abelian varieties over higher dimensional ($> 1$) base schemes $S$, let's say $S$ smooth, separated and of finite type over a field? If not, under what additional conditions? 


This is not answer to the OP, but to the remark of Pete on singular base scheme $S$. Here is an example explainning why one should assume regularity even in dimension $1$. Let $T$ be a smooth curve over a field $k$ and identfity two rational points $t_1\ne t_2$ on $T$. We get a finite birational morphism $T\to S$ of integral curves over $k$. Let $E\to T$ be an elliptic curve with non isomorphic fibers at $t_1, t_2$. Let $\eta$ be the common generic point of $T$ and $S$. Then I claim that $E_\eta$ has no Néron model over $S$. Suppose that we have a Néron model $E'$ over $S$. As $E$ is the Néron model of $E_\eta$ over $T$, we get a birational morphism f: $E'\times_S T\to E$ which is an isomorphism away from $\{ t_1, t_2\}$. Denote by $E_i$ the fiber of $E$ over $t_i$. We have a morphism $f_i : E'_{s}\to E_i$ where $s$ is the image of $t_i$ in $S$.
An idea to construct an example in higher dimension smooth basis: let $S$ be the affine plane containning a nodal curve passing through the origin $o$. Blowup $o$ to get a smooth surface $T$ and consider an elliptic curve $E$ over $T$ with non isomorphic fibers at $t_1, t_2$ (intersection points of the exceptional divisor with the strict transform of the nodal curve). If any abelian scheme is the Néron model of its generic fiber (which seems reasonable if Néron model exists over regular base schemes), then similarily to the above we could prove that the generic fiber of $E$ has no Néron model over $S$. 


Take a family of elliptic curves over the punctured plane whose $j$invariant at $(x,y)$ is $y/x$. Perhaps you should ask if there exists a blowup of $S$ on which a model exists. 

