You can create them manually (I have an example below) or use the imdb lookup feature to create one automatically, then edit it. The important part is the “file” line in the video section, you need to add an attribute called mplayer-options and set it to the extra parameters you want to give mplayer for that particular video.

I use this to crop the black borders from badly encoded videos, which means I can now watch them fullscreen without having to go over to the keyboard and enter huge command lines. Yay.

Here is an example FXD for Batman: Dead End, which if you haven’t seen I suggest you go download as it’s very cool.

Other tools I’m playing with are:
mencoder, doesn’t do 2-pass mpeg2 encoding though.
tovid, seems to want to convert the ac3 audio to mpa so that would have to be redone after.
transcode, don’t think this does 2-pass either but haven’t looked in detail.

This guide looks useful.

Once I’ve got the video and audio into the right format I think qdvdauthor should suffice to generate an iso.

If this all works as I hope it will actually be simpler than the horrid windows method, fingers crossed.