1. Enable RPM Fusion yum repository
The CentOS rpm packages of ffmpeg, mplayer, mencoder and MP4Box are available on RPM Fusion YUM repository. RPM Fusion repo depends on packages from EPEL repo. So enable these repositories by installing following RPM packages:
rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-4.noarch.rpm
rpm -Uvh http://download1.rpmfusion.org/free/el/updates/testing/5/i386/rpmfusion-free-release-5-0.1.noarch.rpm
rpm -Uvh http://download1.rpmfusion.org/nonfree/el/updates/testing/5/i386/rpmfusion-nonfree-release-5-0.1.noarch.rpm
Note: for following ‘yum‘ commands, use the switch –exclude “*.i386″ on 64-bit systems so as to avoid installing both 64-bit and 32-bit packages. Of course, DO NOT use this switch on 32-bit systems 
2. Install ffmpeg, mplayer and mencoder
Install these packages using following yum command:
yum install ffmpeg mplayer mencoder
This will also install various dependency packages like libtheora, libvorbis, libogg, lame, opencore-amr, x264, xvidcore etc
3. Install flvtool2
This rpm package is available on RPM Fusion repo. But it also requires ruby rpms. However, it is not recommend to install ruby rpms on a cpanel server. Cpanel has its own ruby installer script. So install ruby using following cpanel script
/scripts/installruby
Flvtool2 is available as a Ruby Gems package. Use following gem command to install flvtool2:
gem install flvtool2
4. Install MP4Box
MP4Box is provided by gpac package. Install gpac and its library packages:
yum install gpac gpac-libs
5. Install ffmpeg-php
Ffmpeg-php requires ffmpeg development package. Install this package using yum:
yum install ffmpeg-devel
Now download the latest ffmpeg-php package:
wget http://downloads.sourceforge.net/ffmpeg-php/ffmpeg-php-0.6.0.tbz2
Untar this package, build and install it with following commands:
tar xjf ffmpeg-php-0.6.0.tbz2
cd ffmpeg-php-0.6.0
phpize
./configure
make
make install
Common errors:
During ./configure step if you get an error like “ffmpeg headers not found. Make sure ffmpeg is compiled as shared libraries using the –enable-shared option
http://www.aiderpro.com/install-ffmpegmp4boxmplayermencoderflvtool2ffmpeg-php-centos-2/