Hi Tom,
yui_combo.php combines several files for the UI running on the browser side (CSS and JS), to reduce the HTTP hits required to "bootstrap" the UI and, yes, it helps caching the resources in both clients and proxies: it uses public and max-age to force a renewal and it uses a "revision number" in the "path" to invalidate the cache when 1) the theme cache is purged and 2) each time the Moodle instance will be updated in any of its components.
To do its work it makes usage even of HTTP GET params to describe a list of files to be served in one HTTP request so you could include query strings in your caching strategy and this could be an alternative option, to be tested (I still need to create the farm to play with).
HTH,
Matteo