Apps with 'Lossless Muxing' feature

Linear video editor for basic cutting, filtering, encoding, scripting, and batch processing; supports many formats but not for non-linear or montage editing.

Shutter Encoder is a free professional encoding and conversion software for everyone, developed with video editors.

Subler is a Mac OS X application that opens media containers, allows you to add or remove media tracks inside them, and then saves them out again. In the specialized language of the video world, Subler is a “transcoder” or “demuxer” depending on how you use it.