IPOD video will need to be (.mp4) format, there is another format (.M4v)that will work and is what the videos are encoded as when you purchase them from Apple Itunes ... I use "Super" for encoding all video, it is absolutey the best "freeware" there is and rivals many "paid for" encoders. It will encode to and from basically any format you can throw at it, including the DVD .vob files ... just copy them from the DVD drag them into super and encode away... straight to IPOD (mp4 or .m4v). So easy a Hummer, Toyota or Suzuki Driver could do it... :applaudit:
For Flash Video files (.flv) ... hands down nothing beats Sorenson Squeeze for compression, web size and quality, Though it kinda pricey if you don't use it often. "Super" will encode to .flv just not as sweet as Sorenson Squeeze.
AL, for what you want, here is how I would do it...
I would use Super to encode the DVD (.vob) You may have to dig for it, there are usually several .vobs on any one DVD. Look for the largest one. Encode the file to an .mov or .mpeg. Copy it to your hard drive first... I will go much faster. Then I would use Quicktime Pro (I have it for PC) to cut the parts of the movie that I want to use and paste into separate MOV or MPEG files. After you are done pulling out the clips you want, you can then use your favorite software to import them and edit or transition together with your effect of choice and compile audio with as well.
Hope that helps... If you have any questions or run into stumbling blocks.. just ask.
Here is a link for Super and Sorenson
http://www.softpedia.com/get/Multimedia/Video/Encoders-Converter-DIVX-Related/SUPER.shtmlhttp://www.sorensonmedia.com/solutions/sidex/suite_spark.php