It's been a while since I've messed with transcode, so things may have changed, but the one problem I had with transcode, was very poor design of it's syntax/switches. When you've got something that has 4.2 million different ways it can be used from the command line, it's very important that you design a syntax that is both machine, and human parsable.
When I last tried to use it (at least a year ago), it was very difficult to tell which options were referring to which stages of the process (incoming/input, internal, outgoing/output). Mplayer by contrast, always figured everything out for the input side, and had a nice simple -vop -aop to specify the output video/audio plugins and their options. Transcode literally had hundreds and hudreds of switches, all of which had vague or missing documentation.
For my purposes, mplayer is usually a much better tool, just because of it's simplicity. There are only about 3 things I'd ever want to do with a video. 1) make a quick svcd: The shell script that comes with mplayer always worked just fine for me, once I grabbed 2 or 3 things it needed using apt. 2) make a dvd: There is a pike script out there (written by the author of pike) called mkdvd.pike or something like that. It's a dream come true for simple dvd creation. Give it a list of files, a couple a switches to tell it what image to use for the menu background etc, and out comes a dvd.iso file. It uses mplayer as the back end, of course with a few other toys required.. But once again with atrpms/apt they're a synch to install. 3) convert it to a reasonable format for saving (divx?): google -> "mencoder examples" -> I feel lucky.
Kino also works very well for the dv editing side, and will export to dvd/svcd/vcd/etc formatted files, right from the gui.
Transcode is a great bit of software. Lots of projects use it as a back end, and it does a great job of actually handling the video. Someone needs to write a wrapper or something though that makes it more usable from the command line. Maybe the documentation has improved (I hope it has) since I last used it. The author of mkdvd.pike was going to have a switch to allow you to use transcode as the backend instead of mplayer, but he could never figure out all the transcode options to properly support the switches in his script... and let's face it.. He's no slouch.. he did write his own programming language at some point.
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