Handbrake is fine, but the latest version only supports MP4 & MKV.. i never stick to one tool & so i use some other converters based on the requirement
please visit the product websites for full features,
AutoGK ** DVD to AVI/DivX/XVid
http/www.free-codecs.com/download/autogk.htm
AVIRecomp ** resize .avi file & more
i use the tool a lot for resizing avi file , its the one of best tool for avi resizing without loss of quality
http/www.avirecomp.com/page.php?2
video to video converter
all in one converter with tons of features
http
/www.videotovideo.org/
Free videomake converter
*** with an option to limit the output size *****which i want the most of time because of my limited storage capacity..
all in one
http
/www.freemake.com/free_video_converter/
Format factory
all in one along with support for pictures
http
/www.pcfreetime.com/
AVIMux gui **** avi & mkv only
simplest tool to combine several video, audio or subtitle files into one file, with out without size restriction
http/www.alexander-noe.com/video/amg/#features
apart from this i use tools included with Cowon JetAudio *** you can try it if you give more attention to audio effects & audio clarity (((((( which i'm not able to find from any other media players)))))) , SRS Audio Sandbox also gives something special for audio experience( i use older version bcz newer one is messed up)