g@gl:~/Downloads$ ffmpeg -y -i input.mov -acodec libfaac -ar 44100 -ab 96k -vcodec libx264 -level 41 -crf 20 -bufsize 20000k -maxrate 26000k -g 250 -r 20 -s 1280x720 -coder 1 -flags +loop -cmp +chroma -partitions +parti4x4+partp8x8+partb8x8 -flags2 +dct8x8+bpyramid -me_method umh -subq 7 -me_range 16 -keyint_min 25 -sc_threshold 40 -i_qfactor 0.71 -rc_eq 'blurCplx^(1-qComp)' -bf 16 -b_strategy 1 -bidir_refine 1 -refs 6 -deblockalpha 0 -deblockbeta 0 -vpre ~/src/ffmpeg/ffpresets/libvpx-720p output.mp4
libvpx-720p50_60.ffpreset  libvpx-720p.ffpreset
g@gl:~/Downloads$ ffmpeg -y -i input.mov -acodec libfaac -ar 44100 -ab 96k -vcodec libx264 -level 41 -crf 20 -bufsize 20000k -maxrate 26000k -g 250 -r 20 -s 1280x720 -coder 1 -flags +loop -cmp +chroma -partitions +parti4x4+partp8x8+partb8x8 -flags2 +dct8x8+bpyramid -me_method umh -subq 7 -me_range 16 -keyint_min 25 -sc_threshold 40 -i_qfactor 0.71 -rc_eq 'blurCplx^(1-qComp)' -bf 16 -b_strategy 1 -bidir_refine 1 -refs 6 -deblockalpha 0 -deblockbeta 0 -vpre ~/src/ffmpeg/ffpresets/libvpx-720p.ffpreset output.mp4
FFmpeg version 0.6.2-4:0.6.2-1ubuntu1.1, Copyright (c) 2000-2010 the Libav developers
  built on Sep 16 2011 16:57:46 with gcc 4.5.2
  configuration: --extra-version=4:0.6.2-1ubuntu1.1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --enable-shared --disable-static
  WARNING: library configuration mismatch
  libavutil   configuration: --extra-version=4:0.6.2-1ubuntu2 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libdirac --enable-libgsm --enable-libopenjpeg --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-libopenjpeg --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libfaad --enable-libdirac --enable-libfaad --enable-libmp3lame --enable-librtmp --enable-libx264 --enable-libxvid --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavcodec  configuration: --extra-version=4:0.6.2-1ubuntu2+medibuntu1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libdirac --enable-libgsm --enable-libopenjpeg --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-version3 --enable-vaapi --enable-libopenjpeg --enable-libfaac --enable-nonfree --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libfaad --enable-libdirac --enable-libfaad --enable-libmp3lame --enable-librtmp --enable-libx264 --enable-libxvid --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavformat configuration: --extra-version=4:0.6.2-1ubuntu1.1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavdevice configuration: --extra-version=4:0.6.2-1ubuntu1.1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavfilter configuration: --extra-version=4:0.6.2-1ubuntu1.1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libswscale  configuration: --extra-version=4:0.6.2-1ubuntu1.1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libpostproc configuration: --extra-version=4:0.6.2-1ubuntu1.1 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --disable-stripping --enable-runtime-cpudetect --enable-vaapi --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libdc1394 --shlibdir=/usr/lib/i686/cmov --cpu=i686 --enable-shared --disable-static --disable-ffmpeg --disable-ffplay
  libavutil     50.15. 1 / 50.15. 1
  libavcodec    52.72. 2 / 52.72. 2
  libavformat   52.64. 2 / 52.64. 2
  libavdevice   52. 2. 0 / 52. 2. 0
  libavfilter    1.19. 0 /  1.19. 0
  libswscale     0.11. 0 /  0.11. 0
  libpostproc   51. 2. 0 / 51. 2. 0

Seems stream 1 codec frame rate differs from container frame rate: 5994.00 (5994/1) -> 23.98 (2997/125)
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'input.mov':
  Metadata:
    major_brand     : qt
    minor_version   : 537199360
    compatible_brands: qt
  Duration: 00:03:42.18, start: 0.000000, bitrate: 25977 kb/s
    Stream #0.0(eng): Audio: pcm_s16le, 48000 Hz, 2 channels, s16, 1536 kb/s
    Stream #0.1(eng): Video: h264, yuv420p, 1280x720, 24438 kb/s, 23.98 fps, 23.98 tbr, 2997 tbn, 5994 tbc
File for preset '/home/g/src/ffmpeg/ffpresets/libvpx-720p.ffpreset' not found

g@gl:~/Downloads$ ls /home/g/src/ffmpeg/ffpresets/libvpx-720p.ffpreset
/home/g/src/ffmpeg/ffpresets/libvpx-720p.ffpreset