[...insert big 'ar' line here...]
/usr/local/apache/sbin/apxs -c -o libphp3.so dbase/libdbf.a         '-Wl,-rpath /usr/local/lib/mysql' -L/usr/local/lib/mysql -lmysqlclient               -lz       mod_php3.c libmodphp3-so.a
gcc -DLINUX=2 -DMOD_SSL=201106 -DEAPI -O6 -fpic -DSHARED_MODULE -I/usr/local/apache/include  -c mod_php3.c
ld -Bshareable -o libphp3.so mod_php3.o dbase/libdbf.a -Wl,-rpath /usr/local/lib/mysql -L/usr/local/lib/mysql -lmysqlclient -lz libmodphp3-so.a 
ld: unrecognized option `-Wl,-rpath'
apxs:Break: Command failed with rc=65536
make: *** [libphp3.so] Error 1

[after this, I tried the apxs line from 3.0.5...]
/usr/local/apache/sbin/apxs -c -o libphp3.so dbase/libdbf.a         -L/usr/local/lib/mysql -lmysqlclient              -lz   mod_php3.c libmodphp3-so.a   dbase/libdbf.a  -lgdbm         -L/usr/local/lib/mysql -lmysqlclient                -lgd -lz     -lm -ldl -lcrypt -lnsl  -lresolv

[...which worked.  Configuration line:]
CFLAGS=-O6 configure --with-system-regex --with-apxs=/usr/local/apache/sbin/apxs --with-gd --with-mysql --with-zlib --with-dbase --with-config-file-path=/usr/local/apache/etc --enable-safe-mode --with-exec-dir --enable-memory-limit

[3.0.6 exhibits similar behavior (with the addition of the @FDFTK_LIB@ thing)]