What we have done in PE is to use the stylesheet GIUD at the end of the URL as a parameter. Something like this:
<link href="/CMSPages/GetResource.ashx?stylesheetname=SiteCodeName&vid={%GlobalObjects.CssStylesheets.SiteCodeName.StylesheetVersionGUID#%}" type="text/css" rel="stylesheet"/>
It works very well especially since it's tied to the version history of the stylesheet. For the JS files, since they don't have versioning or any history in the database, you're best just appending your own parameter whenever you change it.