Where you don't see this done much is with general-purpose programming languages. This is probably because people who find s-expressions useful are already using Lisp as their general-purpose language. So it's mostly done for interoperability with other, pre-existing systems, like web browsers or C libraries. (You can see an example of the latter on slides 15 and 16 of http://www.xach.com/lisp/lispvan-2008-02-28.pdf.)
Erlang is a fascinating intermediate case. The distinctive value of Erlang is arguably not in the language, but in its runtime and libraries (including Mnesia). For this reason, the "general-purpose" caveat doesn't apply, and it's easy to see why someone might want to build a Lisp program on top of the Erlang runtime via embedded s-expressions. I seem to recall that there was a game company already doing this. If anyone knows about that or other examples, please post them here.
Whenever a language has a burdensome and rigid syntax, isn't there almost necessarily a way to make a good s-expression syntax to substitute it? You'd get macros free!