One thing I like to do with my code is make sure that it's refactored into manageable pieces. However, when it comes to building the software, I find that whatever build automation software I end up using (lately it's been GNU Make or SCons) ends up becoming a complete mess. The input files look like long scripts that seem to defy easy refactoring. I'd like to be able to refactor them in some way, but the concept of "function" doesn't quite behave the same way in some build automation software as it does in a programming language, so I find it difficult to write manageable Makefiles or SConscript files for any projects that are moderately complicated.

Does anyone have any advice on writing manageable input files for build automation software? Software-agnostic advice would be best, but even advice about a specific build automation tool would be helpful, particularly Make or SCons, since that's what I've been using for projects.