I have created a patch against trunk that gets the shared libraries and the applications building with autotools. Currently, this does not build the documentation directory or the test directory, but the basics to the framework is there.
Updated autotools support
The original patch was quite useful to me as it simplifies building on a GNU based system quite a lot. However, I needed support for cross-compilation as well so I've enhanced the original patch by adding support for cross-compilation.
Please consider adding this autotools support to elftoolchain.