I believe that some of the deepest results in the Fourier analysis of groups are
Harish-Chandra's results on the Plancherel formula for semi-simple Lie groups.
If $G$ is a semi-simple Lie group (e.g. the special linear groups $SL_n(\mathbb R)$, the special orthogonal groups $SO(p,q)$, etc.) then $G$ has a unique (up to scaling) translation invariant measure, the so-called Haar measure, and the $L^2$-space with respect to this measure, i.e. $L^2(G)$, is naturally a representation of $G$ under the (left or right, it's your choice) translation action of $G$.
The problem of the Plancherel formula is to decompose $L^2(G)$ into irreducible
representations.
Here are some examples (neither group is semi-simple, actually, but they will give the idea):
If $G$ is the circle group $S^1$, then $L^2(S^1)$ is a (completed) direct sum of the characters $z \mapsto z^n$ (for $n \in \mathbb Z$); this is the theory of Fourier series.
If $G = \mathbb R$ then $L^2(G)$ is the direct integral of the characters $x\mapsto e^{ix y}$ ($y\in \mathbb R$); this is the theory of the Fourier transform.
When $G$ is a non-abelian group like $SL_2(\mathbb R)$ the situation is more complicated, because (a) such groups will admit infinite-dimensional irreducible
representations, which can appear in $L^2$, so $L^2$ won't just decompose into
one-dimensional characters anymore; (b) unlike in the abelian case, where the space of characters is again a group, and hence homogenous, the collection of representations of a semi-simple group won't be homogenous in any sense, and correspondingly, the decomposition of $L^2(G)$ won't be homogeneous — it can contain both direct sum parts (like in the Fourier series case) and direct integral parts (like in the Fourier transform case).
Harish-Chandra determined the Plancherel formula by first finding the direct sum part for every semi-simple group, and then making an inductive argument on the dimension of the group to understand the direct integral part.
Some more details of this picture can be found in this MO answer.
As for applications to physics, I'm not the right person to comment seriously on that . However, it seems worth noting that the unitary irreducible representations of $SL_2(\mathbb R)$ were first classified by Bargmann, who I think was a physicist, and that Harish-Chandra, who was a student of Dirac, began his work by trying to generalize Bargmann's classification to other semi-simple groups.