I have deleted /usr/local/php5.3 and compiled PHP 5.3.1 in directory /usr/local/php5.3.1. After installtion pear creates its pear.conf in /usr/local/php5.3/etc. I always thought that compiling in /usr/local/programname was a clean way because all files are placed within it and not scattered around in the rest of the system. Apparently I'm wrong. Where is the file that pear uses to still create this file in the old directory /php5.3?
edit: doesn't seem to be a pear problem. The extension dir and include path are also wrong (phpinfo). So the --with-prefix=/usr/local/php5.3.1 isn't used for everything.