One source of monoids is given by taking rings with identity, and forgetting about addition.
So similarly, one source of semigroups that are not monoids is taking rings without identity, and forgetting about addition. With this in mind, let me explain one basic source of rings without identity.
A basic source of rings is given by taking functions satisfying some reasonable condition on a space, e.g. continuous real or complex valued functions on a space, with pointwise addition and multiplication. Of course, the constant function 1 is continuous, and so this gives a ring with identity.
But suppose now that we impose some condition, such as "all functions that are continuous, and which furthermore vanish at some specified point". This throws out the constant function 1, and so gives a ring without identity. Now you could naturally object that this is artificial
(as per the requirement in the question that there not be an obvious extension to a monoid),
so let me add more explanation as to why it need not be.
One example of a point to consider is "the point at infinity", i.e. we could look at all functions which vanish at infinity, i.e. which on the complement of larger and larger compact sets, grow smaller and smaller. This is a natural condition to impose in many analytic contexts, and so gives a natural example. (The reason that this kind of growth
condition is natural in analysis is that, on a non-compact space, e.g. the real line, a random continuous function may not be integrable (just as an example), and imposing some decay at infinity (perhaps of the kind I specified, or perhaps something more quantitive) becomes a way to rescue the situation.) (Note also that the example that Tomer Vromen gives is exactly of this form.)
Finally, note that if your semigroup doesn't have an identity, then you can always formally adjoin one, just by throwing in an extra element e and declaring that ex = x for all x.
One can do a similar thing for rings without identity. If A is a C-algebra (say) without an identity, then one can form A + C e (the direct sum), and declare that e acts as a multiplicative identity. This is a frequently-used technique in the theory of rings-without-identity.
P.S. I don't know much literature about semigroups without identity, but for rings without identity, the best literature I know of is in functional analysis books; e.g. Naimark's classic Normed Rings often treats the case of Banach algebras (and the like) without identity in addition to the case when they do have identity, exactly so as to be able to handle examples such as the ring of continuous functions on a locally compact space that vanish at infinity.