If I understand correctly what you are looking for, then yes, a fair amount of work has been done. Deitmar and Hoffman use a simple trace formula on SL(3) to get asymptotics of class number of cubic orders, which can also be interpreted as a prime geodesic theorem. This is a higher-dimensional analogue of quadratic class numbers (which can be viewed as special $L$-values) appearing in a trace formula for SL(2). Deitmar also treats higher rank analogues in other papers.
Another way in which zeta/$L$-functions arise in the geometric side of trace formulas (maybe not what you are looking for, but perhaps still interesting) is discussed in general in this paper of Hoffman and for Sp(4) in his joint paper with Wakatsuki. Namely, one gets Shintani zeta functions arising as coefficients in the unipotent geometric terms of the Arthur-Selberg trace formula.