1. Let $C$ be the category of finite sets with bijections as morphisms. Then we have the functor $\mathrm{Sym} : C \to C$ which maps every set to its set of permutations, 
and the functor $\mathrm{Ord} : C \to C$ which maps every set to its set of total orderings; the action on morphisms is "conjugation". Then we have $\mathrm{Sym}(X) \cong \mathrm{Ord}(X)$ for every $X \in C$, but $\mathrm{Sym} \not\cong \mathrm{Ord}$ (in fact between these functors there is no natural transformation at all).

2. Let $G$ be a group (or monoid), considered as a category with one object $\star$. Then a functor $G \to \mathsf{Set}$ is the same as a $G$-set. In fact, the category of $G$-sets is isomorphic to the category of functors $G \to \mathsf{Set}$. The value at $\star$ is the underlying set. Of course for $G \neq 1$ there are non-isomorphic $G$-sets whose underlying sets are isomorphic (for example the underlying set of $G$ with the regular action and with the trivial action of $G$).

3. If $C$ denotes the category of finite abelian groups, then $\mathrm{Tor}_1^{\mathbb{Z}}$ and $\otimes_{\mathbb{Z}} : C \times C \to C$ are pointwise isomorphic (since $\mathrm{Tor}_1(\mathbb{Z}/n,\mathbb{Z}/m) \cong \mathbb{Z}/\mathrm{gcd}(n,m) \cong \mathbb{Z}/n \otimes_{\mathbb{Z}} \mathbb{Z}/m$), but they are not isomorphic.