Recently I have learned about computing the fundamental group of a graph embedded in $R^3$. The procedure is to find a minimal spanning tree and then consider the free group on all the edges of graph not in this tree.
My question is, what is the usefulness or what are possible applications of associating this group with a graph that tells me something about graphs in general that I can't determine without using algebraic topology?
For instance, it is possible by computing minimal spanning trees of two different graphs and then computing their fundamental groups we can rule out these graphs as isomorphic. But this isn't much more than counting and comparing the number of edges.
So what does knowing the fundamental group of a graph spur us on to?

The computation of the fundamental group of a graph is the first step of the computation of many, many other fundamental groups. For example, for any simplicial complex, or more generally a CW complex $X$, the first step in computing its fundamental group $\pi_1(X)$ is to compute the fundamental group of the 1-skeleton $X^{(1)}$ which is a graph. The final outcome is the calculation of an explicit presentation of the fundamental group of $X$. Intermediate steps steps involve applications of Van Kampen's Theorem, but you can't get off the ground without knowing that the fundamental group of the 1-skeleton is a free group.
Also, the computation of the fundamental group of a graph gives us a powerful topological tool for studying algebraic properties of the free group itself. One example is the theorem that every subgroup of a free group is free. The first step is to take a graph whose fundamental group is the given free group. Subsequent steps use covering space theory to show that every subgroup of the fundamental group is isomorphic to the fundamental group of some other graph (namely a covering space), and hence is a free group.
There is also a whole theory of automorphisms and outer automorphisms of free groups which starts by representing the free group as the fundamental group of a graph, and then goes on to study automorphisms and outer automorphisms by representing those as homotopy equivalences of the graph.
I don't know if that's enough evidence to convince you, but it's just a few tips of a lot of icebergs.