To complete my previous findings on Libtool, I must say that indeed the libtool people provided me with a solution to prevent the C++/Java tests from appearing in configure (it will be in libtool 1.6 but I backported it) and that I found a way to avoid that the C tests are performed twice (I have contributed it to libtool and it will also be in 1.6).

Also, I just updated to the last Automake 1.8 beta, and the new implementation of aclocal saved over 300k on my tarball, so not everything's wrong in the Autotools after all... :-) (aclocal now includes m4 files that are in the distribution directory using m4_include, and not literally in aclocal.m4).