I've worked hard (6 hours) to get ffmpeg working in CentOs 5. It is difficult because examples around are older for both ffmpeg changed and also the CentOs.
Step by step I'll explain (Got the copy of bash_history file):

lets start with removing some packages

yum remove ffmpeg x264 faad2 faad2-devel


and install required packages for development:

yum install gcc gcc-c++ automake autoconf libtool yasm git subversion strace zlib zlib-devel faac-devel lame-devel libvorbis-devel xvidcore-devel


Starting with faad:

wget http://downloads.sourceforge.net/faac/faad2-2.6.1.tar.gz
tar xzf faad2-2.6.1.tar.gz
cd faad2
autoreconf -vif
./configure
make
make install
cd ..


Now GPAC. If system have no mozilla browser, it cant comply unless you ignore the Mozilla part with editing gpac/applications/osmozilla/Makefile . Comment out (put "#" infront of lines)
INSTDIRS+=osmozilla
APPDIRS+=osmozilla


wget http://downloads.sourceforge.net/gpac/gpac-0.4.4.tar.gz
tar -xzvf gpac-0.4.4.tar.gz
cd gpac
chmod a+x configure
./configure
make
make install
make install-lib
cd ..

GPAC installs its files other than expected we should make our system recognize with

echo '/usr/local/lib/' > /etc/ld.so.conf.d/gapc-1386.conf
ldconfig

X264 codec: (infact we follow these steps because x264 is not complied with mp4 output enabled.)

git clone git://git.videolan.org/x264.git
cd x264
./configure --enable-pthread --enable-mp4-output --enable-shared
make
make install

ldconfig
cd ..

The final ffmpeg

svn export svn://svn.mplayerhq.hu/ffmpeg/trunk ffmpeg
cd ffmpeg/
./configure --prefix=/usr/local --disable-debug --enable-shared --enable-gpl --enable-nonfree --enable-postproc --enable-pthreads --enable-x11grab --enable-libx264 --enable-libxvid --enable-libvorbis --enable-libfaac --enable-libfaad --enable-libmp3lame
make
make install

It's all.
ffmpeg -i windows_media_video.wmv -ab 48kb -vcodec libx264 -vpre max -ac 1 -r 20 pretty_flash_video.mp4