Decent introductions can be found in Discovering modern set theory. II, by Weese and Just, and in Introduction to cardinal arithmetic, by Holz, Steffens, and Weitz. Most likely there are a few other presentations at a comparable level.
The technique is so useful that is employed in many arguments, in a large variety of ways, and I fear I would leave out too many references even if I just tried to list relevant examples covering the key applications.
That said, you definitely want to examine arguments related to negative partition relations, that is, arguments establishing the existence of colorings where large sets not only fail to be monochromatic, but actually take as many colors as possible. There are three papers I suggest you look at in this regard: Consider the following theorem:
Suppose $\lambda$ is an uncountable regular cardinal and there is some non-reflecting stationary subset of $\lambda$. Then $\lambda\not\to[\lambda]^2_\lambda$. That is, there is a function $f:[\lambda]^2\to\lambda$ such that whenever $X$ is a subset of $\lambda$ of size $\lambda$, we have that $f[[X]^2]=\lambda$.
This result was proved by Shelah using Todorcevic's method of walks, and it is an elegant elementary substructure argument. See
Saharon Shelah. Was Sierpiński right? I. Israel J. Math., 62 (3), (1988), 355–380. MR0955139 (89m:03037).
The method of walks itself is central to many modern results in infinitary combinatorics. Several key properties (of the so-called $\rho$-functions) are established by elementary substructure arguments. Todorcevic's introduction, where $\omega_1\not\to[\omega_1]^2_{\omega_1}$ is first established, is highly recommended:
Stevo Todorcevic. Partitioning pairs of countable ordinals. Acta Math., 159 (3-4), (1987), 261–294. MR0908147 (88i:04002).
Todorcevic's result was later extended by Moore, showing that we can in fact ensure the existence of an $f:[\omega_1]^2\to\omega_1$ such that for any uncountable $A,B\subseteq\omega_1$, $f[A\otimes B]=\omega_1$, that is, for any $\xi<\omega_1$ there are $\alpha<\beta$, with $\alpha\in A$ and $\beta\in B$ such that $f(\alpha,\beta)=\xi$. This is a key component of his solution to the $L$-space problem:
Justin T. Moore. A solution to the $L$ space problem. J. Amer. Math. Soc., 19 (3), (2006), 717–736. MR2220104 (2008c:54022).
Even here, the list above is severely outdated: For example, there are fairly recent results of Rinot and Rinot-Todorcevic on the "rectangular square-bracket operation", and Stevo has written a beautiful book on the technique of walks, Walks on ordinals and their characteristics. Also, Eisworth-Shelah have extensions to coloring theorems at successors of singular cardinals.
The method of elementary substructures is also used to establish positive partition relations. A very nice paper, fairly readable and a good way of acquiring some intuition on the technique, is
James E. Baumgartner, András Hajnal, Stevo Todorcevic. Extensions of the Erdős-Rado theorem. In Finite and infinite combinatorics in sets and logic (Banff, AB, 1991), pp. 1–17, NATO Adv. Sci. Inst. Ser. C Math. Phys. Sci., 411, Kluwer Acad. Publ., Dordrecht, 1993. MR1261193 (95c:03111).
A direct continuation of the methods used in this paper, but now to establish polarized relations, is in
James E. Baumgartner, András Hajnal. Polarized partition relations, J. Symbolic Logic, 66 (2), (2001), 811–821. MR1833480 (2002k:03068).
A good survey of these methods can also be seen in the Hajnal-Larson paper for the Handbook.
I expect the above directly addresses your question, but I would be remiss if I did not mention that the technique is also used in many forcing arguments. For example, to establish chain conditions. There is also Todorcevic's technique of forcing with models as side conditions, which recently has been used by Friedman and Neeman, independently, to obtain an essentially different proof of the consistency of $\mathsf{PFA}$ relative to a supercompact cardinal, in the process answering a question of mine and others on the reals of inner models of models of $\mathsf{PFA}$.
Again, it would be futile to even attempt to give a reasonably complete list of suggestions here. But I expect the above should give you a good starting point anyway. Let me add that the technique is particularly useful when studying proper and semiproper forcing notions (this is emphasized in the Martin's maximum paper by Foreman, Magidor, and Shelah, for example).
I still hope one day (soon...) to finish a book Boban Velickovic and I started a long while ago. For now, I have posted on my site a short excerpt showing how the techniques of elementary substructures can be used even at a very basic level.
(A more sophisticated application by Boban and I can be seen in this paper.)