File formats etc...

how can I tell the encoder to leave them in?

If you're using the command-line LAME, read the MAN page. If you're using a GUI I don't know, but there's a lowpass filter control that you can set wherever you want if you break it open and manage the commands manually. I don't remember where anything is, unfortunately, but it's all in the MAN pages (or readme, if you're using those pathetic, inferior non-Linux operating systems) if you look.

Jeff
 
To get back to the question of the thread-starter: I would encode an MP3 with LAME @ -V 0.
Why? Because Trent Reznor did so with his latest free release and he surely is the man! :D :p