>>199
とりあえず、、、試してみた。
topdirのMakefile.am (プログラム名はhooと仮定)

SUBDIRS = others
bin_PROGRAMS = foo
foo_SOURCES = main.c
foo_LDDADD = $(top_builddir)/othes/libhoo.la
foo_CFLAGS = -I$(top_srcdir)/others
foo_LDFLAGS = -L$(top_builddir)/others -lhoo

othersのMakefile.am

lib_LTLIBRARIES = libhoo.la
libhoo_la_SOURCES = hoo.c hoo.h

configure.ac

AC_PREREQ(2.61)
AC_INIT([foo], [0.0.0], [nanasi@example.com])
AC_CONFIG_SRCDIR([main.c])
AC_CONFIG_HEADER([config.h])
AM_INIT_AUTOMAKE([foreign])
AC_PROG_CC
AC_PROG_LIBTOOL
AC_CONFIG_FILES([Makefile
others/Makefile])
AC_OUTPUT