For those that would rather not deal with writing command lines or fussing with containers and codecs, I find the VLC player works just fine. Say you've got a full 90 minute movie in a huge file. As per Sturgeon's Law, 90% of everything is crap. If you're lucky, there may be about 9 minutes of footage you'd ever want to see again. Just open the file w/ the VLCPlayer, move the slider to the start of the section you want to keep and click the red Record button. When you come to wherever you want the clip to end, click the square Stop button. Bingo...a file is saved as "vlc-record-(today's date) (time of recording) (original filename) .mp4". Or .avi, or .flv etc. works great for any type of file, even .vob. Pop in a 2 hour DVD...go thru and edit out your favorite parts...the file is saved as (filename).vob. Just rename the file as (filename) .mpg and you're good to go. Got yourself a handful of 2 or 3 minute clips w/out all the rest of the junk there on the disc.
The best part....it's free.
http://www.videolan.org/vlc/index.html