The thing is depend what you are trying to do. To compress DVD/Blurays, I find handbrake invaluable, because it will automatically deal all kind of weird corner cases in term of pixel format, image ratio, cropping, deinterlacing, etc, that I don't have to write in a command line on every new file (and every disk seems to be doing something different).

But if you are dealing with repeatable, consistent file format (like files coming from the same camera), you are way better off going the command line route, and chances are the command will be pretty simple.