To add a remark related to Jim Belk's answer and the OP's comments on that answer:
In many naturally occurring situations, including some of those where group theory is particularly useful, endomorphisms are automatically automorphisms.
For example, if $E/F$ is a finite extension of fields, any endomorphism of $E$ which is the identity on $F$ is automatically an automorphism of $E$.
As another example, if $C$ is a Riemann surface of genus at least $2$, then
any (nonconstant) endomorphism of $C$ is necessarily an automorphism.
Any endomorphism of a Euclidean space which preserves lengths is necessarily an automorphism.
Another point to bear in mind is that the groups that arise in practice in geometry are often Lie groups (i.e. have a compatible topological, even smooth manifold, structure). One can define a more general notion of Lie semigroup,
but if your Lie semigroup has an identity (so is a Lie monoid) and the semigroup
structure is non-degenerate in some n.h. of the identity, then Lie semigroup
will automatically be a Lie group (at least in a n.h. of the identity). A related remark: in the definition of a formal group, there is no need to include an
explicit axiom about the existence of inverses.
To make a point related to Qiaochu Yuan's answer: in some contexts semigroups
do appear naturally.
For example, studying the rings of endomorphisms of an object is a very common technique in lots of areas of mathematics. (E.g., just
to make a connection to my first point, for genus $1$ Riemann surfaces, there can be endomorphisms that aren't automorphisms, but then genus $1$ Riemann surfaces can also be naturally made into abelian groups --- so-called elliptic curves --- and there is a whole theory, the theory of complex multiplication, devoted to studying their endomorphisms rings.)
As another example, any ring of char. $p > 0$ has a Frobenius endomorphism, which is not an automorphism in general; but the semigroup of endomorphisms
that it generates is typically an important thing to consider in char. $p$ algebra and geometry. (Of course, this semigroup is just a quotient of $\mathbb N$.)
One thing to bear in mind is what you hope to achieve by considering the group/semigroup of automorphisms/endomorphisms.
A typical advantage of groups is that they admit a surprisingly rigid theory (e.g. semisimple Lie groups can be completely classified; finite simple groups can be completely classified), and so if you discover a group lurking in your particular mathematical context, it might be an already well-known object, or at least there might be a lot of known theory that you can apply to it to obtain greater insight into your particular situation.
Semigroups are much less rigid, and there is often correspondingly less that can be leveraged out of discovering a semigroup lurking in your particular context. But this is not always true; rings are certainly well-studied, and the appearance of a given ring in some context can often be leveraged to much advantage.
A dynamical system involving just one process can be thought of as an action of the semigroup $\mathbb N$. Here there is not that much to be obtained from
the general theory of semigroups, but this is a frequently studied context. (Just to give a perhaps non-standard example, the Frobenius endomorphism of a char. $p$ ring is such a dynamical system.)
But, in such contexts, precisely because general semigroup theory doesn't help much, the tools used will be different.
E.g. in topology, the Lefschetz fixed point theorem is a typical tool that is used to study an endomorphism of (i.e. discrete dynamical system on) a
topological space. Interestingly, the same formula is used to study the action of Frobenius in char. $p$ geometry (see the Weil conjectures). So even in contexts
such as action of the semigroup $\mathbb N$, there is some coherent philosophy that can be discerned --- it is just that it is supplied by topology rather than algebra, since the algebra doesn't have all that much to say.
I think the conclusion to be drawn is not to be too doctrinaire, and to be sensitive to the actual mathematical contexts in which and from which the various notions of group, semigroup, automorphism, and endomorphism arise and have arisen.
I had a little go at reading it. The paper is a mess with like $20$ help-variables together with the original $4$ defined randomly throughout making it almost impossible to follow. Finding the mistake(s) is not easy, but I think I have found a serious flaw.
The main part of the argument (his first proof) starts at page 4 (before it is just the special case $c,c' = 1$). Without using anywhere the fact that the variables have to be integers and by just defining new variables and making simple manipulations the author arrives at the result (mid-page 6) that if $Y^p = X^q + 1$ then $X^p = 4$. The only assumption is that $c = \frac{X^p - 1}{Y^{p/2}}\not= 1$ and $c' =\frac{7-X^p}{Y^{p/2}}\not= 1$. By the method used this should also hold if $X,Y,p,q$ are real numbers which is obviously wrong.
I should note that there is a possibillity that the author have been using hidden assumptions / deductions (i.e. using divisibillity properties without saying so). If this is the case then it becomes impossible to follow so at best we can say that the proof is flawed. Another issue is that the author uses cases without naming them so we have arguments like “But .. thus .. and .. hence .. thus .. or .. also .. and .. hence .. or .. and .. or .. and .. and .. hence”. What is in each case / subcase is hard to read from this. To reach the conclusion above I have tried to read the cases and sub cases as they are most naturally interpreted.
Best Answer
For myself I would like to bring up Leonard Lewin's Polylogarithms and associated function. In chapter $2$, dealing with the Inverse Tangent Integral, Catalan's Constant is introduced:
Fascinating about this constant I would claim is especially its broad occurrence within many, on the first sight distinct, problems of closed-form integration aswell as closed-form summation. As José Carlos Santos already pointed out: whilst taking into account how less we know about this real number it is odd how widely it can be used.
I firstly encoutered this constant in the context of Dilogarithms, to be precise by invoking auxiliary functions such as the aforementioned Inverse Integral Tangent or the Clausen Functions, and the Dirichlet Beta Function which both tend to be possible defintions for the constant in terms of an infinite series, namely
Even though this sum looks pretty similiar to the Riemann Zeta Function and its relatives it cannot be related to them that simple $($the only possible functional relation I am aware of is given within this article but hence it uses the Polygamma Functions aswell I would not call this relation "easy" as e.g. the one between the Riemann Zeta Function and the Dirichlet Eta Function$)$. To speak for myself the different "character" of the Dirichlet Beta Function, i.e. having expressible values for odd positive integers, not being expressable with the help of the Riemann Zeta Function alone, etc., justifies its importance.
Of course, only to appear everywhere is not a criterion for being important alone but appearing over and over again, especially in connection with $\pi$, seems to imply that there is something more about this number. Concerning the appearance I would like to refer to this question here on MSE dealing with the relationship between Catalan's Constant and $\pi$ in particular.
To bring up another point showing the importance of Catalan's Constant I would claim that its role can be compared with the role of Apéry's Constant $\zeta(3)$. Both can be defined in terms of infinite series, namely the Dirichlet Beta Function and the Riemann Zeta Function respectively. Both are the first positive integers for which the underlying Function cannot be expressed using other constants. As already mentioned there are formulae for the even positive integer values of the Riemann Zeta Function and for the odd positive integer values of the Dirichlet Beta Function given by
Whereas we defined $\beta(2)$ as Catalan's Constant and $\zeta(3)$ as Apéry's Constant. A crucial different, however, is that we know that the latter constant is in fact irrational due to Apéry who proved this back in $1979$. Interesting enough a similiar series representation for $G$ exists like the one Apéry used within his proof. These series are given by
All in all Catalan's Constant does not only occurs in a bunch of mathematical problems related to integration and summation but also plays a quite important role in the field of Zeta Functions and relatives. I would say especially the striking parallels between Apéry's Constant and Catalan's Constant consolidate the importance of this constant.