I've solved the problem for the moment adding LDFLAGS:

LDFLAGS=-L/usr/X11/lib ./configure --with-mysql=/opt/ ...

but I doubt that is the elegant solution.

What's your configure line?

Did you use --with-t1lib-dir?

Below is the config command. I did not use --with-t1lib-dir for two reasons: 
1) I thought that was for only for t1lib, which is found
2) It's not only a problem compiling t1lib. If I disable
   t1lib in the config, the same problem appears with
   another library (also because of not finding freetype)

LDFLAGS=-L/usr/X11/lib ./configure --with-mysql=/opt/mysql --with-apxs --with-ming --with-zlib --with-bz2 --enable-exif --enable-ftp --with-gd --enable-gd-native-ttf --with-ttf=/usr/X11 --with-freetype-dir=/usr/X11 --enable-sockets --with-t1lib --with-truetype --prefix=/usr --enable-mbstring --with-libxml-dir=/opt/gnome

Please use the t1lib directive and run the configure without LD_FLAGS.

"If I disablet1lib in the config, the same problem appears with another library (also because of not finding freetype)"

Can you be more clear? Please paste the exact errors here, and which libraries do not work, for which extensions.

adding:
--with-t1lib=/usr/local

same error:
checking for FreeType 1 support... no - FreeType 2.x is to be used instead
checking for T1_StrError in -lt1... no
configure: error: Problem with libt1.(a|so). Please check config.log for more information.

The --with-t1lib-dir directive you asked for does not appear in ./configure --help, so I suspect it has to be the above directive (--with-t1lib=...)

Then, disabling --without-t1lib, I get the error:

checking for iconv in -liconv... no
configure: error: Please reinstall the iconv library.

which, again, is not the fault of not finding iconv, but
not finding freetype (according to the config.log):

configure:45338: gcc -o conftest -g -O2   -Wl,-rpath,/opt/gnome/lib -L/opt/gnome
/lib conftest.c -liconv  -lfreetype -lpng -lz -lbz2 -lz -lresolv -lm -ldl -lnsl -lxml2 -lz -lm -lxml2 -lz -lm 1>&5                                             
/usr/lib/gcc/i686-pc-linux-gnu/3.4.6/../../../../i686-pc-linux-gnu/bin/ld: cannot find -lfreetype

Sorry, but your problem does not imply a bug in PHP itself.  For a
list of more appropriate places to ask for help using PHP, please
visit http://www.php.net/support.php as this bug system is not the
appropriate forum for asking support questions.  Due to the volume
of reports we can not explain in detail here why your report is not
a bug.  The support channels will be able to provide an explanation
for you.

Thank you for your interest in PHP.

"configure: error: Problem with libt1.(a|so). Please check config.log for more information."

Did you install the t1lib develpement package?

"checking for iconv in -liconv... no
configure: error: Please reinstall the iconv library.
which, again, is not the fault of not finding iconv, but
not finding freetype (according to the config.log):"

No, you are missing iconv or the development packages (-devel or whatever it is on your platform).

I do not see something about freetype not found, only that it will use freetype2.

What you pasted here from your config.log is sadly useless. However, it is clear that you did not install everything required to compile PHP. It is not a bug.