Depends on your processing environment. Many XML parsers allow you to specify an EntityResolver or XmlResolver as a callback to process and resolve external entity references. Layered on top of this, you will find parsers or other utilities that support OASIS catalogs, which allow you to define indirections for entity references in an XML catalog file.
Personally, I prefer not to use entity references for this kind of application, but to use custom markup instead. (Some people prefer XLink/XInclude, but I prefer to roll my own.) It's then very easy to process the links/transclusions using XSLT. A particular benefit is that it's hard to transform XML while leaving the entity references intact, but it becomes very easy to leave links intact if they use logical (element-level) markup.