The end is pretty easy. An element of the end is a choice of endomorphism $\alpha_S$ for each set $S$, such that the endomorphisms commute with all functions: for any $f: S \to T$, $f \circ \alpha_S = \alpha_T \circ f$. It's clear that $\text{id}$, the collection of identity maps, is such an element. Also, if we choose $S = \{*\}$ then it's clear that $\alpha_T$ must fix every $t \in T$. So the end has only the single element $\text{id}$.
The coend (as others have said) is harder. But here's a pretty good description. I think it's equivalent to @Kyle Miller's, but with some details filled in.
We have the functor $\operatorname{Hom}: \operatorname{Set}^{\operatorname{op}} \times \operatorname{Set} \to \operatorname{Set}$. The coend $\int^S \operatorname{Hom}(S, S)$ would be a set with maps $i_X: \operatorname{Hom}(X, X) \to \int^X$ for all $X$, which is a universal cowedge.
For the "universal" part, we just take $\coprod_X \operatorname{Hom}(X, X)$.
For "cowedge", we need the square
from $\operatorname{Hom}(Y, X) \to \int^S$ to commute for any $f: X \to Y$.
That is, $i_X \cdot (- \cdot f) = i_Y \cdot (f \cdot -)$, where $- \cdot f: \operatorname{Hom}(Y, X) \to \operatorname{Hom}(X, X) $ and $f \cdot -: \operatorname{Hom}(Y, X) \to \operatorname{Hom}(Y, Y)$.
The cowedge condition gives a relation between endomorphisms of sets: if we have endomorphisms $\phi$ of $X$ and $\psi$ of $Y$, and if they are related via functions $f:X \to Y$ and $g: Y \to X$ such that $gf = \phi$ and $fg = \psi$, we will say $\phi W \psi$.
Then $\int^S$ would be $\coprod_X \operatorname{Hom}(X, X) / \sim$, where $\sim$ is the equivalence relation generated by $W$.
So our main goal is to describe $\sim$.
(Here we are taking a coproduct over a proper class, but we will ignore size issues throughout.)
Here's a description of $\sim$. Fix an endomorphism $\sigma$ in $\operatorname{Set}$. We'll describe the equivalence class $[\sigma]$ under $\sim$.
Some endomorphisms are conjugate: for endomorphisms $\phi_0$, $\phi_1$ of $X_0$, $X_1$ respectively, we will say $\phi_0 \simeq \phi_1$ if there is an isomorphism $\alpha: X_0 \to X_1$ such that $\phi_1 = \alpha \phi_0 \alpha^{-1}$. For $i \ge 0$, define $D^i$ as all $\phi$ such that $\phi | _{\phi^i[X] \to \phi^i[X]} \simeq \sigma$ (where $\phi: X \to X$). Then define $D = \bigcup_i D^i$.
I claim that $[\sigma] = D$.
First we show $[\sigma] \subseteq D$. Clearly $\sigma \in D^0$. So it's enough to show that for $i \ge 0$, if $\phi \in D^i$ and $\phi W \psi$, then $\psi \in D^{i + 1}$. So suppose we have $X$, $Y$, $f$, $g$ witnessing $\phi W \psi$. Take $\bar X = \phi^i[X]$ and $\bar \phi = \phi | _{\bar X \to \bar X}$, so $\bar \phi \simeq \sigma$. Take $\bar Y = f[\bar X]$, and note $g[\bar Y] = \bar X$, so we can define $\bar f = f | _{\bar X \to \bar Y}$ and $\bar g = g | _{\bar Y \to \bar X}$. Then $\bar \phi = g | _{f[\bar X]} f | _{\bar X} = \bar g \bar f$. Since $\bar \phi$ is an automorphism, $\bar f$ is mono; and $\bar f$ is epi by construction, and therefore an isomorphism. And $\bar g = \bar \phi {\bar f}^{-1}$ is also an isomorphism.
Now take $\bar \psi = \psi | _{\bar Y \to \bar Y}$. Not surprisingly, $\bar \psi = f | _{gf[\bar X]} g | _{f[\bar X]} = \bar f \bar g$. Note that $\psi^{i + 1} = f \phi^i g$. So we have $\psi^{i + 1}[Y] \subseteq f \phi^i[X] = f[\bar X]$. But also $\psi^{i + 1}[Y] \supseteq f \phi^i g[\bar Y] = f \phi^i[\bar X] = f[\bar X]$. So $\psi^{i + 1}[Y] = f[\bar X] = \bar Y$. Now $\psi | _{\psi^{i + 1}[Y] \to \psi^{i + 1}[Y]} = \psi | _{\bar Y \to \bar Y} = \bar \psi = \bar f \bar g \simeq \bar g(\bar f \bar g){\bar g}^{-1} = \bar \phi \simeq \sigma$. This means $\psi \in D^{i + 1}$ as required, so $[\sigma] \subseteq D$.
To show $D \subseteq [\sigma]$, we need to show that all $D^i \subseteq [\sigma]$, so again we work by induction. If $\phi \in D^0$, then $\phi \simeq \sigma$, so $\alpha \phi \alpha^{-1}$ for some $\alpha$; then taking $f = \alpha \phi$ and $g = \alpha^{-1}$, we see that $\phi W \sigma$. So $D^0 \subseteq [\sigma]$. Now suppose $D^i \subseteq [\sigma]$ for some $i \ge 0$, and $\psi \in D^{i + 1}$. I claim there is a $\phi \in D^i$ with $\phi W \psi$; this gives $\psi \in [\sigma]$, so $D^{i + 1} \subseteq [\sigma]$ as required.
Say $\psi: Y \to Y$. Take $X = \psi[Y]$, and the epi-mono factorization $f: X \hookrightarrow Y$, $g = \psi | _{Y \to \psi[Y]}$ of $\psi = fg$. Take $\phi = gf = \psi | _{X \to X}$. We get $\phi^i[X] = \psi^i[X] = \psi^{i + 1}[Y]$, so $\phi | _{\phi^i[X]} = \psi | _{\psi^{i + 1}[Y]}$. Since $\psi | _{\psi^{i + 1}[Y]} \simeq \sigma$, we get $\phi | _{\phi^i[X]} \simeq \sigma$ and $\phi \in D^i$, as required. So $D \subseteq [\sigma]$, and $D = [\sigma]$. Q.E.D.
In particular, it's easy to describe the two simplest elements of $\int^S$. If $\sigma$ is the endomorphism of the empty set, then it's easy to check that $[\sigma]$ is just the one element $\{\sigma\}$. And if $\sigma$ is the endomorphism of a singleton, then $[\sigma]$ is the class of endomorphisms $\phi$ which are "eventually constant" in the sense that some $\phi^i$ is constant.
The argument also works in $\operatorname{FinSet}$. In this case, the iterated image $\phi[X], \phi^2[X], ...$ eventually settles on a stable subset, so we find that $\phi \sim \sigma$ for an automorphism $\sigma$ of that subset. This means $\int^S$ is the set of conjugacy classes of permutations, or the set of integer partitions.
This appears to be the only reasonably complete answer to the original question.
EDITED to add the coend description.