Indeed, quivers first appeared in the context of D-branes at (conifold) singularities (there are various nice expositions in Klebanov-Witten theory reviews) where the D-branes "conspire" to give a N=1 SYM theory. Additionally, gauge theories are strongly encoded inside the physics of D-branes, so I am not sure in what way you can "separate" these notions. Usually, quivers are used to describe the physics of BPS bound states of N=2 susy and sugra. I will say a few words on this as an example of quivers in gauge theories. So let us consider N=2 theory in four dimensions. As you will probably know this theory has a moduli space with a Coulomb and a Higgs branch. Let us consider a point u in the Coulomb branch C of the moduli space. There we have a gauged U(1)r symmetry group together with a lattice Γ from which the various BPS states take their charges (p,q). From Seiberg-Witten theory we know how to consider the above on an elliptic curve Σu that varies along C. It is very well known that the homology classes of 1-cycles along the tori we are considering can be identified with Γ. This is all standard Seiberg-Witten stuff. Seiberg-Witten is of course solved in the IR. To study the BPS states at some specific point u∈C we need to introduce the quiver. These theories also have a central charge Z. Now, we take half the plain of the plane on which the central charge Z takes values and we name it H. On this plane there exist a set of 2r+f (where f is the number of flavors of the theory) states which are customary to denote as γi (that we can naively consider them as particles). It turns out that such a basis, if it exists, it is the only possible one, it is unique. Using this basis, the set {γi} we can construct a quiver. For every γi we draw a node and for every pair we draw arrows that connect them. Then we can use quiver quantum mechanics to find the BPS bound states of the BPS "particles" γi. So the moral/summary is the following: In the N=2 theory consider a point u of the Coulomb branch and use its data to form (if possible) a basis {γi} of the hypers. Then put a node on each one, and arrows between them. Then use quiver quantum mechanics to find the BPS bound states.