ffmpeg -i 00728.MTS -c:v libx264 -c:a aac output.mp4

Cambiar audio a aac por si acaso:

ffmpeg -i 00728.MTS -c:v copy -c:a aac 00728.mp4

http://forum.videolan.org/viewtopic.php?t=50767

http://www.reelseo.com/html5-ogg-h264-encoding-tools/

ffmpeg -i input.avi -sameq -ar 44100 output.flv

sameq: misma calidad que origen

Si no lo pones se ve muy pixelado

ffmpeg -y -i VID_20111004_210741.3gp -sameq -f mpeg -s cif -r 25 -ar 32000 -ac 1 file.mpg

$ mplayer VID_20111004_210741.3gp 
MPlayer 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team
mplayer: could not connect to socket
mplayer: No such file or directory
Failed to open LIRC support. You will not be able to use your remote control.

Playing VID_20111004_210741.3gp.
libavformat file format detected.
[mov,mp4,m4a,3gp,3g2,mj2 @ 0x9b91620]multiple edit list entries, a/v desync might occur, patch welcome
[lavf] stream 0: audio (aac), -aid 0, -alang eng
[lavf] stream 1: video (h264), -vid 0
VIDEO:  [H264]  720x480  24bpp  90000.000 fps  1123.2 kbps (137.1 kbyte/s)
Clip info:
 major_brand: isom
 minor_version: 0
 compatible_brands: isom3gp4
open: No such file or directory
[MGA] Couldn't open: /dev/mga_vid
open: No such file or directory
[MGA] Couldn't open: /dev/mga_vid
[VO_TDFXFB] Can't open /dev/fb0: Permission denied.
[VO_3DFX] Unable to open /dev/3dfx.
Failed to open VDPAU backend libvdpau_nvidia.so: cannot open shared object file: No such file or directory
[vdpau] Error when calling vdp_device_create_x11: 1
==========================================================================
Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family
Selected video codec: [ffh264] vfm: ffmpeg (FFmpeg H.264)
==========================================================================
==========================================================================
Opening audio decoder: [faad] AAC (MPEG2/4 Advanced Audio Coding)
AUDIO: 32000 Hz, 2 ch, s16le, 96.0 kbit/9.38% (ratio: 12000->128000)
Selected audio codec: [faad] afm: faad (FAAD AAC (MPEG-2/MPEG-4 Audio))
==========================================================================
AO: [pulse] 32000Hz 2ch s16le (2 bytes per sample)
Starting playback...
Movie-Aspect is 1.50:1 - prescaling to correct movie aspect.
VO: [xv] 720x480 => 720x480 Planar YV12 
A:  13.9 V:  13.9 A-V:  0.000 ct:  0.016   0/  0 11%  1%  1.2% 2 0