Arranging Multi-Language Source Code Trees?

jodonn queries: "Often software developers are called upon to write code in multiple languages for a single project. For instance, I've had to write Java applications with C hooks into legacy native applications and batch processes primarily in C++ with some additional code in Perl, and of course I have to support the build process for all these things, often across platforms using Make and Ant. I'd like to hear some tips about best practices when laying out the source code hierarchy for situations like these, with an eye toward ease in compiling and deployment."