If you are using boost-m4 like I do, you can try:
./configure.ac:
BOOST_REQUIRE([1.61])
BOOST_SYSTEM
BOOST_TEST
./test/Makefile.am (add AM_CPPFLAGS, AM_LDFLAGS and LDADD)
AM_CPPFLAGS = $(BOOST_CPPFLAGS) -DBOOST_TEST_DYN_LINK
AM_LDFLAGS = $(BOOST_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS)
LDADD = $(BOOST_SYSTEM_LIBS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS)
check_PROGRAMS = test1 test2
SOURCES = test1.cpp test2.cpp
CC = g++
TESTS = $(check_PROGRAMS) standalone1.test standalone2.test
EXTRA_DIST = $(TESTS)
This seems to be more elegant than directly putting '-lboost_unit_test_framework' inside your Makefile.am. You may also consider moving '#define BOOST_TEST_DYN_LINK' from your cpp to AM_CPPFLAGS in Makefile.am as shown above.
For more details, refer to boost-m4 README