[root@test php-5.3.6]# ./configure --with-apxs2=/usr/local/apache2/bin/apxs --with-mysql
loading cache ./config.cache
checking for Cygwin environment... no
checking for mingw32 environment... no
checking for egrep... grep -E
checking for a sed that does not truncate output... /bin/sed
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for icc... no
checking for suncc... no
checking whether gcc and cc understand -c and -o together... yes
checking how to run the C preprocessor... gcc -E
checking for AIX... no
checking whether ln -s works... yes
checking for system library directory... lib
checking whether to enable runpaths... yes
checking if compiler supports -R... no
checking if compiler supports -Wl,-rpath,... yes
checking for gawk... gawk
checking for bison... no
checking for byacc... no
checking for bison version... invalid
configure: warning: bison versions supported for regeneration of the Zend/PHP parsers: 1.28 1.35 1.75 1.875 2.0 2.1 2.2 2.3 2.4 2.4.1 2.4.2 2.4.3 (found: none).
checking for re2c... no
configure: warning: You will need re2c 0.13.4 or later if you want to regenerate PHP parsers.
checking whether to enable computed goto gcc extension with re2c... no
checking whether to force non-PIC code in shared modules... yes
checking whether /dev/urandom exists... yes
checking for pthreads_cflags... -pthread
checking for pthreads_lib...

Configuring SAPI modules
checking for AOLserver support... no
checking for Apache 1.x module support via DSO through APXS... no
checking for Apache 1.x module support... no
checking whether to enable Apache charset compatibility option... no
checking for Apache 2.0 filter-module support via DSO through APXS... no
checking for Apache 2.0 handler-module support via DSO through APXS...

Sorry, I cannot run apxs.  Possible reasons follow:

1. Perl is not installed
2. apxs was not found. Try to pass the path using --with-apxs2=/path/to/apxs
3. Apache was not built using --enable-so (the apxs usage page is displayed)

The output of /usr/local/apache2/bin/apxs follows:
./configure: line 6355: /usr/local/apache2/bin/apxs: No such file or directory
configure: error: Aborting