ffmpeg

ffmpeg -video_size 1024x768 -framerate 25 -f x11grab -i :0.0+100,200 output.flv

ffmpeg version 2.1.3 Copyright (c) 2000-2013 the FFmpeg developers
  built on Jan 15 2014 20:51:13 with gcc 4.8.2 (GCC) 20131219 (prerelease)
  configuration: --prefix=/usr --disable-debug --disable-static --enable-avresample --enable-dxva2 --enable-fontconfig --enable-gnutls --enable-gpl --enable-libass --enable-libbluray --enable-libfreetype --enable-libgsm --enable-libmodplug --enable-libmp3lame --enable-libopencore_amrnb --enable-libopencore_amrwb --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-librtmp --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libv4l2 --enable-libvorbis --enable-libvpx --enable-libx264 --enable-libxvid --enable-pic --enable-postproc --enable-runtime-cpudetect --enable-shared --enable-swresample --enable-vdpau --enable-version3 --enable-x11grab
  libavutil      52. 48.101 / 52. 48.101
  libavcodec     55. 39.101 / 55. 39.101
  libavformat    55. 19.104 / 55. 19.104
  libavdevice    55.  5.100 / 55.  5.100
  libavfilter     3. 90.100 /  3. 90.100
  libavresample   1.  1.  0 /  1.  1.  0
  libswscale      2.  5.101 /  2.  5.101
  libswresample   0. 17.104 /  0. 17.104
  libpostproc    52.  3.100 / 52.  3.100
[x11grab @ 0x1b04700] device: :0.0+100,200 -> display: :0.0 x: 100 y: 200 width: 1024 height: 768
[x11grab @ 0x1b04700] shared memory extension found
Input #0, x11grab, from ':0.0+100,200':
  Duration: N/A, start: 1390627745.792116, bitrate: 629145 kb/s
    Stream #0:0: Video: rawvideo (BGR[0] / 0x524742), bgr0, 1024x768, 629145 kb/s, 25 tbr, 1000k tbn, 25 tbc
[swscaler @ 0x1aee9c0] deprecated pixel format used, make sure you did set range correctly
Output #0, flv, to 'output.flv':
  Metadata:
    encoder         : Lavf55.19.104
    Stream #0:0: Video: flv1 (flv) ([2][0][0][0] / 0x0002), yuv420p, 1024x768, q=2-31, 200 kb/s, 1k tbn, 25 tbc
Stream mapping:
  Stream #0:0 -> #0:0 (rawvideo -> flv)
Press [q] to stop, [?] for help
frame=   13 fps=3.0 q=24.3 Lsize=     566kB time=00:00:04.40 bitrate=1053.9kbits/s
video:566kB audio:0kB subtitle:0 global headers:0kB muxing overhead 0.072509%