1. Add additional config options to build script:

# http://stackoverflow.com/questions/1604470/cross-compile-apache-portable-runtime-to-the-iphone
my $config_opts = "ac_cv_file__dev_zero=\"yes\" " .
        "ac_cv_func_setpgrp_void=\"yes\" " .
        "apr_cv_process_shared_works=\"yes\" " .
        "apr_cv_mutex_robust_shared=\"no\" " .
        "apr_cv_tcp_nodelay_with_cork=\"yes\" " .
        "ac_cv_sizeof_struct_iovec=\"8\" " .
        "apr_cv_mutex_recursive=\"yes\" " .
        "ac_cv_func_fdatasync=\"no\"";

./iphone.configure --$arch $config_opts

Note that if were to enable bitcode, please add flags -O3 -fembed-bitcode to CFLAGS, else just -O3.

2. Create a iphone.configure file for autotools:

#! /bin/bash

#
# Program  : iphone3.1-configure
# Authors  : Michael Aaron Safyan (michaelsafyan@gmail.com)
# Synopsis :
#            This program runs the "configure" script generated by the
#            GNU Autotools in order to cross-compile thirdparty libraries
#            for the iPhone 3.1 SDK. Run this script while in a directory
#            containing an autotools "configure" script. Once you run this,
#            you can use "make" and "sudo make install" to build the library.
#            An install prefix of "/opt/iphone-3.1/" is used.
#

unset CPATH
unset C_INCLUDE_PATH
unset CPLUS_INCLUDE_PATH
unset OBJC_INCLUDE_PATH
unset LIBS
unset DYLD_FALLBACK_LIBRARY_PATH
unset DYLD_FALLBACK_FRAMEWORK_PATH

export BUILD_DARWIN_VER=`uname -r`
export SDKVER="3.1"
export DEVROOT="/Developer/Platforms/iPhoneOS.platform/Developer"
export SDKROOT="$DEVROOT/SDKs/iPhoneOS$SDKVER.sdk"
export PKG_CONFIG_PATH=/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS$SDKVER.sdk/usr/lib/pkgconfig:/Developer/Platforms/iPhoneOS.platform/Developer/usr/lib/pkgconfig:/opt/iphone-$SDKVER/lib/pkgconfig:/usr/local/iphone-$SDKVER/lib/pkgconfig
export PREFIX="/opt/iphone-$SDKVER"
export AS="$DEVROOT/usr/bin/as"
export ASCPP="$DEVROOT/usr/bin/as"
export AR="$DEVROOT/usr/bin/ar"
export RANLIB="$DEVROOT/usr/bin/ranlib"
export CPPFLAGS="-pipe -no-cpp-precomp -I$SDKROOT/usr/lib/gcc/arm-apple-darwin9/4.2.1/include/ -I$SDKROOT/usr/include -I$DEVROOT/usr/include -I/opt/iphone-$SDKVER/include -I/usr/local/iphone-$SDKVER/include"
export CFLAGS="-std=c99 -arch armv6 -pipe -no-cpp-precomp --sysroot='$SDKROOT' -isystem $SDKROOT/usr/lib/gcc/arm-apple-darwin9/4.2.1/include/ -isystem $SDKROOT/usr/include -isystem $DEVROOT/usr/include -isystem /opt/iphone-$SDKVER/include -isystem /usr/local/iphone-$SDKVER/include"
export CXXFLAGS="-std=c99 -arch armv6 -pipe -no-cpp-precomp --sysroot='$SDKROOT' -isystem $SDKROOT/usr/lib/gcc/arm-apple-darwin9/4.2.1/include/ -isystem $SDKROOT/usr/include -isystem $DEVROOT/usr/include -isystem /opt/iphone-$SDKVER/include -isystem /usr/local/iphone-$SDKVER/include"
export LDFLAGS="-arch armv6 --sysroot='$SDKROOT' -L$SDKROOT/usr/lib -L$DEVROOT/usr/lib -L/opt/iphone-$SDKVER/lib -L/usr/local/iphone-$SDKVER/lib"
export CPP="$DEVROOT/usr/bin/cpp"
export CXXCPP="$DEVROOT/usr/bin/cpp"
export CC="$DEVROOT/usr/bin/gcc-4.2"
export CXX="$DEVROOT/usr/bin/g++-4.2"
export LD="$DEVROOT/usr/bin/ld"
export STRIP="$DEVROOT/usr/bin/strip"

if [ ! \( -d "$DEVROOT" \) ] ; then
   echo "The iPhone SDK could not be found. Folder \"$DEVROOT\" does not exist."
   exit 1
fi

if [ ! \( -d "$SDKROOT" \) ] ; then
   echo "The iPhone SDK could not be found. Folder \"$SDKROOT\" does not exist."
   exit 1
fi

./configure --prefix="$PREFIX" --build="i386-apple-darwin$BUILD_DARWIN_VER" --host="arm-apple-darwin9" --enable-static --disable-shared ac_cv_file__dev_zero=no ac_cv_func_setpgrp_void=yes $@

3. Patch the header file, in apr/include/apr_general.h, add the following line to line 35:

#include <stddef.h>

Or you could apply the following patch file:

--- a/source/apr/include/apr_general.h
+++ b/source/apr/include/apr_general.h
@@ -33,6 +33,8 @@
 #include <signal.h>
 #endif
 
+#include <stddef.h>
+
 #ifdef __cplusplus
 extern "C" {
 #endif /* __cplusplus */

4. If run into Bad CPU type in executable error, do the following steps to manually compile gen_test_char (refer to https://stackoverflow.com/questions/18408400/apache-cross-compilation-error-gen-test-char-cannot-execute-binary-file):
   a. cd $APR/tools
   b. gcc -Wall -O2 -DCROSS_COMPILE gen_test_char.c -s -o gen_test_char
   c. cd ..
   d. make install