How do I add and/or keep subtitles when converting video?

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http://askubuntu.com – I have a mkv video I want to convert to mp4, but every which way I try and convert it (Handbrake, WinFF, ffmpeg, mencoder,...I lose the video's subtitles. How can I convert the video,keeping the subtitles, or add a subtitles.srt? I also would like 2 pass encoding with a video bitrate of 3556 and audio bitrate of 160. Thanks. (HowTos)