The notion of an ultrapower and more generally reduced powers and their generalizations are essentially category theoretic. More specifically, reduced powers are essentially pro-sets. This answer is a part of my own research, but these results are not ready to publish yet. Although these results relate the ultrapower construction to categories, I do not see how these results could generalize to possibly relate ultraproducts to categories.
In the other answers to this question, people have explained how ultraproducts are direct limits. It turns out that reduced powers are directed limits as well. Furthermore, I will show that as categories, the category of generalized reduced powers is equivalent to the category of inverse systems of sets. By the category of generalized reduced powers, I mean the category of most model-theoretic generalizations of the ultrapower and reduced power construction such as extenders, iterated ultrapowers, limit ultrapowers 3, Boolean ultrapowers 4, and their reduced power analogues such as limit reduced powers.
If $\mathcal{C}$ is a category, then the category $\mathbf{Pro}(\mathcal{C})$ is essentially the category of inverse systems over the category $\mathcal{C}$ and it should be thought of as the category of inverse limits from the category $\mathcal{C}$. I claim that the category $\mathbf{Pro}(\mathbf{Set})$ of pro-sets is equivalent to a full subcategory of pro-filters. Furthermore, these pro-filters are the things that we want to construct reduced powers. In fact, we obtain a three way duality between the category of pro-sets, the full subcategory of pro-filters where the transitional mappings are epimorphisms, and categories of reduced powers of structures.
$\large\mathbf{Categories}$
In this section, I will first define the categories and I will state the equivalences between these categories.
Let $A$ be a fixed infinite set. Let $\Omega(A)$ be the algebra with universe $A$ and where every operation is a fundamental operation. Then every object in $V(\Omega(A))$ is isomorphic to a limit reduced power of $\Omega(A)$ and any elementary extension of $\Omega(A)$ is isomorphic to a limit ultrapower of $\Omega(A)$ (see 3 for information on limit ultrapowers). Also, one may represent algebras in $V(\Omega(A))$ as limit reduced powers in such a way so that the homomorphisms between algebras in $V(\Omega(A))$ are induced by mappings between the underlying sets of the limit reduced powers. Since every algebra in $V(\Omega(A))$ is isomorphic to a limit reduced power of of $\Omega(A)$, one should think of the algebras in $V(\Omega(A))$ as limit reduced powers.
A small nonempty category $D$ is said to be a cofiltrant category if whenever $e_{1},e_{2}\in D$, then there is some $d\in D$ and morphisms $\ell_{1}:d\rightarrow e_{1},\ell_{2}:d\rightarrow e_{2}$, and if $\ell_{1},\ell_{2}:d\rightarrow e$ are morphisms, then there is some object $c$ and a morphism $m:c\rightarrow d$ with $\ell_{1}m=\ell_{2}m$. Every downward directed set is a cofiltrant category, and the notion of a cofiltrant category is the categorization of the notion of a downward directed set.
If $\mathcal{C}$ is a category, then $\mathbf{Pro}(\mathcal{C})$ is the category of all functors $F:\mathcal{D}\rightarrow\mathcal{C}$ for some cofiltrant category $\mathcal{D}$. One should think of the category $\mathbf{Pro}(\mathcal{C})$ as the category of all inverse limits in $\mathcal{C}$ since the notion of a cofiltrant category is the categorization of the notion of a downward directed set.
If $F:\mathcal{D}\rightarrow\mathcal{C},G:\mathcal{E}\rightarrow\mathcal{C}$ are objects in $\mathbf{Pro}(\mathcal{C})$, then define the set of morphisms by
$$\mathrm{Hom}(F,G)=\varprojlim_{e\in\mathcal{E}}\ \varinjlim_{d\in\mathcal{D}}\ \mathrm{Hom}(F(d),G(e)).$$
The transitional mappings in the direct and inverse limits are the canonical ones, and the definition of composition of morphisms is defined in the natural way.
The following categories are the object of study in the papers 1 and 2.
We shall now construct a category $\mathfrak{F}$. The objects in $\mathfrak{F}$ are pairs
$(X,\mathcal{F})$ where $X$ is a set and $\mathcal{F}$ is a filter on $X$. If $(X,\mathcal{F}),(Y,\mathcal{G})\in\mathfrak{F}$, then function $f:X\rightarrow Y$ is a morphism from $(X,\mathcal{F}),(Y,\mathcal{G})$ if $f^{-1}[R]\in\mathcal{F}$ whenever $R\in\mathcal{G}$. It is easy to show that $f$ is a morphism from $(X,\mathcal{F})$ to $(Y,\mathcal{G})$ if and only if whenever $R\subseteq X$ is non-negligible (i.e. $R^{c}\not\in\mathcal{F}$), then the image $f[R]$ is non-negligible. The intuition behind defining the category $\mathfrak{F}$ this way is that we do not want to map non-negligible sets to negligible sets since that is like a function mapping a non-empty set to an empty set.
Let $\mathfrak{G}$ be the quotient category of $\mathfrak{F}$ where we relate two morphisms if they differ by a negligible set. In other words, the objects in $\mathfrak{G}$ and $\mathfrak{F}$ are the same. If $(X,\mathcal{F}),(Y,\mathcal{G})$ are objects in $\mathfrak{F}$, and $f,g\in\mathrm{Hom}_{\mathfrak{F}}[(X,\mathcal{F}),(Y,\mathcal{G})]$, then $f\simeq g$ iff $\{x\in X|f(x)=g(x)\}\in\mathcal{F}$. Then $\mathrm{Hom}_{\mathcal{G}}[(X,\mathcal{F}),(Y,\mathcal{G})]=\mathrm{Hom}_{\mathfrak{F}}[(X,\mathcal{F}),(Y,\mathcal{G})]/\simeq$. The composition in $\mathfrak{G}$ is defined in the obvious manner.
While the categories $\mathfrak{F}$ and $\mathfrak{G}$ were both studied in 1 and 2, the category $\mathfrak{G}$ is more fundamental than $\mathfrak{F}$ and the category $\mathfrak{G}$ deserves to be called the category of filters while $\mathfrak{F}$ does not seem to be very useful.
Morphisms between algebras in $\mathfrak{G}$ induce homomorphisms between reduced powers. If $\mathcal{A}$ is an algebraic structure and $[f]:(X,\mathcal{F})\rightarrow(X,\mathcal{G})$ is a morphism in $\mathfrak{G}$, then we define a morphism $[f]^{\bullet}:\mathcal{A}^{X}/\mathcal{G}\rightarrow\mathcal{A}^{Y}/\mathcal{F}$ by letting $[f]^{\bullet}[\ell]=[\ell\circ f]$.
$\mathbf{Proposition}$ Let $[f]\in \mathrm{Hom}_{\mathfrak{G}}[(X,\mathcal{F}),(Y,\mathcal{G})]$. The
following are equivalent.
If $[f]$ is an epimorphism in $\mathfrak{G}$.
$\mathcal{G}=\{S\subseteq Y|f^{-1}[S]\in\mathcal{F}\}$
If $R\in\mathcal{F}$, then $f[R]\in\mathcal{G}$.
The canonical mapping $[f]^{\bullet}:A^{Y}/\mathcal{G}\rightarrow A^{X}/\mathcal{F}$ is injective for each set $A$.
Let $\mathbf{PF}$ be the full subcategory of $\mathbf{Pro}(\mathfrak{G})$ whose objects consist of inverse systems $((X_{d},\mathcal{F}_{d})_{d\in D},(\ell_{d_{1},d_{2}})_{d_{1}\leq d_{2}})$ over directed sets $D$ such that each $\ell_{d_{1},d_{2}}$ is an epimorphism in $\mathfrak{G}$.
$\mathbf{Humor}:$ I call the objects in $\mathbf{PF}$ pro-filters. That is, professional filters. The pro-filters play football in the National Filter League (NFL).
If $\kappa$ is a cardinal, then let $\mathbf{PF}_{\kappa}$ denote the full subcategory of $\mathbf{PF}$ consisting of inverse systems $(X_{d},\mathcal{F}_{d})_{d\in D}$ such that $|X_{d}|<\kappa$ for each $d\in D$. Let $\mathbf{Set}_{\kappa}$ denote the category of sets of cardinality less than $\kappa$. Let $\mathbf{U}_{\kappa}$ be the subcategory of $\mathbf{PF}_{\kappa}$ consisting of all inverse systems $(X_{d},\mathcal{F}_{d})_{d\in D}$ where each $\mathcal{F}_{d}$ is an ultrafilter.
$\mathbf{Theorem}$ Let $A$ be an infinite set.
The category $\mathbf{PF}$ is covariantly equivalent to the category $\mathbf{Pro}(\mathbf{Set})$.
The functor defined by $(X_{d},\mathcal{F}_{d})_{d\in D}\mapsto \Omega(A)^{X_{d}}/\mathcal{F}_{d}$ is a contravariant equivalence
between the category $\mathbf{PF}_{|A|^{+}}$ and the category
$V(\Omega(A))$. Furthermore, this functor restricts to an equivalence
between the category $\mathbf{Pro}(\mathbf{U}_{|A|^{+}})$ and the
elementary extensions of $\Omega(A)$.
The category $\mathbf{Pro}(\mathbf{Set}_{|A|^{+}})$ is contravariantly equivalent to the category $V(\Omega(A))$.
The equivalences between the category $\mathbf{PF}$ and $\mathbf{Pro}(\mathbf{Set})$ can be described explicitly. If $((X_{d},\mathcal{F}_{d})_{d\in D},(\ell_{d_{1},d_{2}})_{d_{1}\leq d_{2}})\in\mathbf{PF}$, then add a transitional mapping $f:X_{d}\rightarrow X_{e}$ whenever $f\in\textrm{Hom}_{\mathfrak{F}}((X_{d},\mathcal{F}_{d}),(X_{e},\mathcal{F}_{e}))$ and $[f]=\ell_{d,e}$.
If $F:\mathcal{D}\rightarrow\mathbf{Set}$ is a pro-set, then for each $d\in\mathcal{D}$, then $\{\mathrm{Im}(F(f))|f:e\rightarrow d\,\textrm{for some}\,e\in\mathcal{D}\}$ is a filterbase that generates a filter on $F(d)$ which we shall denote by $\mathcal{F}_{d}$.
Partial order $\mathcal{D}$ where $d\leq e$ iff there is a morphism from $d$ to $e$. Then if $d\leq e$, then let $\ell_{d,e}:(X_{d},\mathcal{F}_{d})\rightarrow(X_{e},\mathcal{G}_{e})$ be the morphism where
$\ell_{d,e}=[F(f)]$ for some $f:d\rightarrow e$. It is easy to show that the morphism $\ell_{d,e}$ does not depend on $[F(f)]$ and $((X_{d},\mathcal{F}_{d}),(\ell_{d,e})_{d\leq e})\in\mathbf{PF}$.
$\mathbf{Corollary}$ If $|A|<|B|$, then the category $V(\Omega(A))$ is
equivalent to a full subcategory of $V(\Omega(B))$.
$\mathbf{Corollary}$ If $(X_{d},\mathcal{F}_{d})_{d\in
D},(Y_{e},\mathcal{G}_{e})_{e\in E}\in\mathbf{PF}_{|A|^{+}}$, and the algebras
$^{\lim}_{\longrightarrow}\Omega(A)^{X_{d}}/\mathcal{F}_{d}$ and
$^{\lim}_{\longrightarrow}\Omega(A)^{Y_{e}}/\mathcal{G}_{e}$ are
isomorphic, then
$^{\lim}_{\longrightarrow}\mathcal{A}^{X_{d}}/\mathcal{F}_{d}$ and
$^{\lim}_{\longrightarrow}\mathcal{A}^{Y_{e}}/\mathcal{G}_{e}$ are
isomorphic for each structure $\mathcal{A}$.
The above result still holds when one replaces the direct limit of reduced powers with other reduced power and ultrapower constructions.
$\large\textbf{An Application}$
We shall now give an application that shows that going between algebras and different categories may be useful. The following result can be proved using the duality between pro-filters and algebras (the proof also uses a version of the Feferman-Vaught theorem, and the Keisler-Shelah isomorphism theorem or Frayne's theorem).
$\mathbf{Theorem}$ Let $\mathbf{2}$ denote the two element Boolean
algebra. Let
$\mathcal{A}\mapsto\mathbf{R}(\mathcal{A}),\mathcal{A}\mapsto\mathbf{S}(\mathcal{A})$
be two distinct reduced power constructions(such as limit reduced
powers, Boolean powers etc.). If $\mathbf{R}(\mathbf{2})$ and
$\mathbf{S}(\mathbf{2})$ are elementarily equivalent, then there is a
sequence of ultrafilters $\mathcal{U}_{n}$ such that for every
structure $\mathcal{A}$, we have
$$^{\lim}_{n\rightarrow\infty}(\mathbf{R}(\mathcal{A}))^{\mathcal{U}_{0}\cdots\mathcal{U}_{n}}\simeq^{\lim}_{n\rightarrow\infty}(\mathbf{S}(\mathcal{A}))^{\mathcal{U}_{0}\cdots\mathcal{U}_{n}}.$$
We take note that in the above result we cannot replace the direct limit of ultrapowers with a single ultrapower. For example, if $\mathcal{U}$ is a non-principal ultrafilter, and
$\mathbf{R}(\mathcal{A})=\mathcal{A}$ and $\mathbf{S}(\mathcal{A})=\mathcal{A}^{\mathcal{U}}$ for all structures $\mathcal{A}$, then for each non-principal ultrafilter $\mathcal{V}$, we have $\mathcal{V}<_{RK}\mathcal{U}\cdot\mathcal{V}$. In particular, the ultrafilters
$\mathcal{V}$ and $\mathcal{U}\cdot\mathcal{V}$ are not Rudin-Kiesler equivalent, so there is some structure $\mathcal{A}$ where the structures $\mathcal{A}^{\mathcal{V}}$ and $\mathcal{A}^{\mathcal{U}\cdot\mathcal{V}}\simeq(\mathcal{A}^{\mathcal{U}})^{\mathcal{V}}$ are not isomorphic.
I must also mention that the elementary classes of Boolean algebras have a particularly nice and simple classification. There is a countable set of Boolean algebra invariants called the elementary invariants, and two Boolean algebras are elementarily equivalent if and only if they satisfy the same elementary invariants. In particular, to check that $\mathbf{R}(2)$ and $\mathbf{S}(2)$ are elementarily equivalent, it suffices to show that these Boolean algebras have the same elementary invariants. The reader is referred to [5] or [6][Vol. 1] for more information on these elementary invariants.
Oh the joy of cats!!!
1 Blass, Andreas
Two closed categories of filters.
Fund. Math. 94 (1977), no. 2, 129–143.
2 Koubek, Vaclav; Reiterman, Jan
On the category of filters.
Comment. Math. Univ. Carolinae 11 1970 19–29
3 Keisler, H. Jerome. Limit ultrapowers.
Trans. Amer. Math. Soc. 107 1963 382–408
4 Mansfield, Richard. The theory of Boolean ultrapowers.
Ann. Math. Logic 2 (1970/71), no. 3, 297–323.
[5] Chang, Chen Chung, and H. Jerome Keisler. Model Theory. Amsterdam: North-Holland Pub., 1973.
[6] Monk, J. Donald, Robert Bonnet, and Sabine Koppelberg. Handbook of Boolean Algebras. Amsterdam: North-Holland, 1989.