Just tried to compile PHP 5.3.6 with using the --with-libdir option. The compile process always failed because either libpng.(a|so) or libjpeg.(a|so) was not found:

# ./configure --prefix=/usr --with-libdir=/usr/lib64 --with-gd ....
...
checking for FreeType 2... no
checking for T1lib support... no
checking whether to enable truetype string function in GD... yes
checking whether to enable JIS-mapped Japanese font support in GD... no
checking for fabsf... (cached) yes
checking for floorf... (cached) yes
If configure fails try --with-jpeg-dir=<DIR>
configure: error: libpng.(a|so) not found.

But libpng.so exists:

# ls -l /usr/lib64/ | grep png
lrwxrwxrwx  1 root root       10 Feb  7 11:43 libpng.a -> libpng12.a
lrwxrwxrwx  1 root root       11 Feb  7 11:43 libpng.so -> libpng12.so
lrwxrwxrwx  1 root root       13 Jul 17  2010 libpng.so.3 -> libpng12.so.0
-rw-r--r--  1 root root   242636 Jul 17  2010 libpng12.a
lrwxrwxrwx  1 root root       18 Feb  7 11:43 libpng12.so -> libpng12.so.0.27.0
lrwxrwxrwx  1 root root       18 Jul 17  2010 libpng12.so.0 -> libpng12.so.0.27.0
-rw-r--r--  1 root root   153072 Jul 17  2010 libpng12.so.0.27.0

Even a configure with the option --with-png-dir=/usr/lib64 didn't work.

The solution is not to use the full path in the --with-libdir option, but only the folder name of the library folder:

# ./configure --prefix=/usr --with-libdir=lib64 --with-gd ....
...
checking for FreeType 2... no
checking for T1lib support... no
checking whether to enable truetype string function in GD... yes
checking whether to enable JIS-mapped Japanese font support in GD... no
checking for fabsf... (cached) yes
checking for floorf... (cached) yes
If configure fails try --with-jpeg-dir=<DIR>
checking for png_write_image in -lpng... (cached) yes
If configure fails try --with-xpm-dir=<DIR>
If configure fails try --with-freetype-dir=<DIR>
checking for GNU gettext support... yes
...

Unfortunately there is nothing written about this in ./configure --help.