Seems like you upgraded PHP to newer version and old .ini files are still pointing to old location.
The solution: find out where are modules located now
ls -l /usr/lib/php5
There should be a directory similar to old 20090626. In my case it is now 20131226
The .ini files giving you an error are located at /etc/php5/cli/conf.d/
Just edit those .ini files which module gives you an error. For example, in case the error is for mcrypt module:
sudo vi /etc/php5/cli/conf.d/20-mcrypt.ini
Change the line:
extension=/usr/lib/php5/20090626/mcrypt.so
to reflect the new path for .so file. In my case the correct path should be:
extension=/usr/lib/php5/20131226/mcrypt.so
That's it! The error is gone. Ofc you'd have to do it with each module giving you an error.
suhosinandidnmodules got removed in this newer packages.. so big thx for the nicegrepline.