Had this warning when I installed php5.2.6
------------------------------------------------------
Notice: Following unknown configure options were used:

--enable-gd
--enable-track-vars
--enable-trans-id
--with-cpdflib=/usr/local
--enable-ssl

Check './configure --help' for available options

[root@zimbra php-5.2.6]#
-------------------------------------------------------

Are these flags still on the latest version of php? Has anybody experienced same problems?

I installed everything from source, all latest versions. apache 2.2.10, and openssl-0.9.8i.

Here's what I did on the PHP installation
./configure \
--prefix=/usr/local/php \
--exec-prefix=/usr/local/php \
--with-libxml-dir=/usr/local/libxml2 \
--with-apxs2=/usr/local/apache2.2/bin/apxs \
--libexecdir=/usr/local/apache2.2/lib/apache \
--with-config-file-path=/usr/local/apache2.2/conf \
--with-mysql=/usr/local/mysql \
--with-mysqli=/usr/local/mysql/bin/mysql_config \
--with-mysql-sock=/tmp/mysql.sock \
--with-sqlite \
--enable-sqlite-utf8 \
--with-pgsql=/usr/local/pgsql \
--with-zlib \
--with-zlib-dir \
--with-gd \
--enable-gd-native-ttf \
--with-jpeg-dir=/usr/local \
--with-png-dir=/usr/local \
--with-ttf \
--with-freetype-dir=/usr/local \
--with-iconv=/usr/local \
--with-curl=/usr/local \
--enable-track-vars \
--with-gettext \
--enable-trans-id \
--enable-ftp \
--with-cpdflib=/usr/local \
--enable-mbstring \
--enable-ssl \
--with-openssl

These options are actually invalid.
To get a complete list of possible compile options, execute:

./configure --help

As you will see there, there is no --enable-ssl, nor --enable-gd
You can use instead --with-openssl=PATH_TO_OPENSSL_DIR

Hope that helps