ld: unrecognized option `-Wl,-rpath'
apxs:Break: Command failed with rc=65536

Looks like apxs is really picky about the order of it's options.  I'm not sure how it happened, but on both the RH Linux and Solaris 2.5.1 machines I tried it on (compiling with imap and mysql to work with apache 1.3.6 and 1.3.4) the arguments to apxs are given out of order by the make file.

The way I found to correct the problem is to move the three actual filenames to the end of the line (mod_php3.o libmodphp3-so.a pcrelib/libpcre.a) then it sings like a bird.

Here's my configure line for the RH 6.0 box:
./configure --prefix=/sys/php --without-gd --with-config-file-path=/sys/php/etc --with-exec-dir=/sys/php/php-bin --with-apxs=/usr/sbin/apxs --with-imap=../imap-4.6.BETA-devel --enable-memory-limit --with-mysql=/sys/mysql

Which generates the following apxs line:
/usr/sbin/apxs -c -o libphp3.so -I. -I. mod_php3.c libmodphp3-so.a -L/usr/local/lib -Wl,'-rpath /sys/mysql/lib' -lgdbm -Wl,'-rpath ../imap-4.6.BETA-devel/lib' -L../imap-4.6.BETA-devel/lib -lc-client  pcrelib/libpcre.a  -L/sys/mysql/lib -lmysqlclient -lpam -lm -ldl -lcrypt -lnsl  -lresolv -Lpcrelib -lpcre