Aug 2017

This command only changes the container, it does not transcode the video/audio.

  ffmpeg -i in.mov -vcodec copy -acodec copy out.mp4

To specify bit rates:

  ffmpeg -i input.mov -b:v 1M -b:a 192k output.mp4

This example converts a .MOV input file, to a h264 output file at 300Mbs.

  ffmpeg.exe -i sourcefile.mov -vcodec h264 -b:v 300M -b:a 240K outputfile.mp4

It's important to get the files correct, initially I specified .mpg on the output and had pages and pages of errors, when I changed the output to .mp4 it worked perfectly with 0 errros.

The output from this was:

ffmpeg version N-82597-gd316b21 Copyright (c) 2000-2016 the FFmpeg developers
  built with gcc 5.4.0 (GCC)
  configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-dxva2 --enable-libmfx --enable-nvenc --ena
ble-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-
libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enab
le-libmodplug --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopenh264 --enable-li
bopenjpeg --enable-libopus --enable-librtmp --enable-libschroedinger --enable-libsnappy --enable-libsoxr --enable-libspe
ex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx
 --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-libzi
mg --enable-lzma --enable-decklink --enable-zlib
  libavutil      55. 40.100 / 55. 40.100
  libavcodec     57. 66.106 / 57. 66.106
  libavformat    57. 58.100 / 57. 58.100
  libavdevice    57.  2.100 / 57.  2.100
  libavfilter     6. 67.100 /  6. 67.100
  libswscale      4.  3.101 /  4.  3.101
  libswresample   2.  4.100 /  2.  4.100
  libpostproc    54.  2.100 / 54.  2.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'falun_1080_50.mov':
  Metadata:
    creation_time   : 2015-02-24T13:36:55.000000Z
  Duration: 00:04:31.40, start: 0.000000, bitrate: 364409 kb/s
    Stream #0:0(eng): Video: prores (apch / 0x68637061), yuv422p10le(bt709, progressive), 1920x1080, 364404 kb/s, SAR 1:
1 DAR 16:9, 50 fps, 50 tbr, 50 tbn, 50 tbc (default)
    Metadata:
      creation_time   : 2015-02-24T13:36:55.000000Z
      handler_name    : Apple Alias Data Handler
      encoder         : Apple ProRes 422 HQ
      timecode        : 01:00:00:00
    Stream #0:1(eng): Data: none (tmcd / 0x64636D74) (default)
    Metadata:
      creation_time   : 2015-02-24T13:47:36.000000Z
      handler_name    : Apple Alias Data Handler
      timecode        : 01:00:00:00
No pixel format specified, yuv422p for H.264 encoding chosen.
Use -pix_fmt yuv420p for compatibility with outdated media players.
[libx264 @ 000000000065bb60] using SAR=1/1
[libx264 @ 000000000065bb60] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX
[libx264 @ 000000000065bb60] profile High 4:2:2, level 5.1, 4:2:2 8-bit
[libx264 @ 000000000065bb60] 264 - core 148 r2721 72d53ab - H.264/MPEG-4 AVC codec - Copyleft 2003-2016 - http://www.vid
eolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed
_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=6 lookah
ead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_
adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40 intra_refresh=0 rc_lookahe
ad=40 rc=abr mbtree=1 bitrate=300000 ratetol=1.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'falun2.mp4':
  Metadata:
    encoder         : Lavf57.58.100
    Stream #0:0(eng): Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv422p, 1920x1080 [SAR 1:1 DAR 16:9], q=-1--1, 30
0000 kb/s, 50 fps, 12800 tbn, 50 tbc (default)
    Metadata:
      creation_time   : 2015-02-24T13:36:55.000000Z
      handler_name    : Apple Alias Data Handler
      timecode        : 01:00:00:00
      encoder         : Lavc57.66.106 libx264
    Side data:
      cpb: bitrate max/min/avg: 0/0/300000000 buffer size: 0 vbv_delay: -1
Stream mapping:
  Stream #0:0 -> #0:0 (prores (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame=13570 fps=3.3 q=-1.0 Lsize=10188596kB time=00:04:31.34 bitrate=307602.8kbits/s speed=0.066x
video:10188308kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.002818%
[libx264 @ 000000000065bb60] frame I:69    Avg QP: 0.45  size:1563111
[libx264 @ 000000000065bb60] frame P:3420  Avg QP: 1.23  size:1243319
[libx264 @ 000000000065bb60] frame B:10081 Avg QP: 3.03  size:602403
[libx264 @ 000000000065bb60] consecutive B-frames:  0.8%  0.2%  0.5% 98.5%
[libx264 @ 000000000065bb60] mb I  I16..4: 16.3% 25.5% 58.3%
[libx264 @ 000000000065bb60] mb P  I16..4:  4.5% 11.8% 14.7%  P16..4: 23.5% 24.6% 20.1%  0.0%  0.0%    skip: 0.7%
[libx264 @ 000000000065bb60] mb B  I16..4:  1.0%  4.0%  3.0%  B16..8: 24.3%  7.7%  6.8%  direct:19.2%  skip:34.0%  L0:31
.9% L1:21.0% BI:47.0%
[libx264 @ 000000000065bb60] final ratefactor: -2.95
[libx264 @ 000000000065bb60] 8x8 transform intra:42.6% inter:39.7%
[libx264 @ 000000000065bb60] coded y,uvDC,uvAC intra: 98.9% 99.5% 99.3% inter: 68.0% 64.4% 64.2%
[libx264 @ 000000000065bb60] i16 v,h,dc,p:  8% 10% 58% 23%
[libx264 @ 000000000065bb60] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 16% 18% 38%  4%  4%  4%  5%  4%  7%
[libx264 @ 000000000065bb60] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 17% 16% 19%  8%  9%  8%  9%  7%  9%
[libx264 @ 000000000065bb60] i8c dc,h,v,p: 60% 11% 22%  7%
[libx264 @ 000000000065bb60] Weighted P-Frames: Y:0.2% UV:0.0%
[libx264 @ 000000000065bb60] ref P L0: 47.1% 13.3% 22.3% 17.2%  0.0%
[libx264 @ 000000000065bb60] ref B L0: 79.7% 14.0%  6.3%
[libx264 @ 000000000065bb60] ref B L1: 94.7%  5.3%
[libx264 @ 000000000065bb60] kb/s:307526.22