This will stream copy (re-mux) all streams:
ffmpeg -i input -map 0 -c copy output.mp4
This will re-encode the video to H.264 and stream copy the audio:
ffmpeg -i input.ts -c:v libx264 -c:a copy output.mp4
The next example will re-encode both video and audio:
ffmpeg -i input.ts -c:v libx264 -c:a aac output.mp4
Lossless H.264 example:
ffmpeg -i input.ts -c:v libx264 -crf 0 -c:a copy output.mp4
WARNING: Lossless files will be huge.
See FFmpeg Wiki: H.264 for more info.