FreeSMUG review: here - HandBrake site: here - HandBrake 0.6 How-To
A Command Line Interface guide here.

Page index:

• Welcome to HandBrake
  
• Source
• Destination
• Video
• Subtitles
• Picture settings...
• Audio
• iPod video settings
• Queue tasks
• How do I play files created by HandBrake

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Intro

Most video files have at least two different types: the container, and the codec(s) used inside that container.

• File Format (container): describes the structure of the file; Handbrake can create MP4, AVI, and OGM file formats.
• Codec ("compressor/decompressor"): is the mathematical routine that compresses the raw video and audio into a stream of bytes.
  
  

  Handbrake container/codecs table
  File format	MP4	AVI	OGM
  Video codec	MPEG-4 AVC/H.264	MPEG-4 AVC/H.264	MPEG-4
  Audio codec	AAC	AC-3 MP3	Vorbis MP3

  
  
• Encoder: is how the data is written into each frame. Each codec will support one or more encoders.
  H.264 has: Main and Baseline. MPEG-4 has: FFmpeg and XviD.

Links:
MPEG-4 AVC/H.264 Information
MPEG-4 ASP Information
Ogg Theora Information
Digital Video Formats by Akkana Peck
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Use WM9 today and get Micro$oft controlling the A/V market tomorrow for free.
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Insert your DVD and quit DVD player.

Welcome to HandBrake

• Start HandBrake.
  Select your DVD volume (generally only one)...

• ... or browse to your folder with VIDEO_TS exctracted from DVD.

• Click Open button and HandBrake will start DVD scan for some seconds.

Source

• In Source panel select the DVD title, the longest is the first of the list and all (default) or one/some chapter/s.

Destination

• In Destination panel select File format (file container) and video Codecs:

MP4 file format

• MP4 file - MPEG-4 video / AAC audio (MPEG)- the Apple audio video format (not DivX)
• MP4 file - AVC H264 video / AAC audio (MPEG)- the Apple audio video format QuickTime 7 - Advanced Video Coding (AVC) for the next-generation High Definition (HD) DVD (*)

AVI file format

• AVI file - MPEG-4 video/ MP3 audio (Lame) - the used DivX players .AVI file
• AVI file - MPEG-4 video/ AC-3 audio - 
• AVI file - AVC H264 video / MP3 audio (Lame) -
• AVI file /- AVC H.264 video / AC-3 audio -
  

OGM file format

• OGM file - MPEG-4 video / Vorbis audio (OGG)- the open, patended free audio/video format (*)
• OGM file - MPEG-4 video / MP3 audio (Lame) - 

(*) We invite you use and spread these free and open formats, they are best quality than other ones.

• Then Browse your hard disk to select file destination folder.

Video

• In Video panel chose encoder; we suggest FFmpeg instead of XviD, as both are MPEG-4 compliant encoders, FFmpeg is pretty faster on OS X.
  

• Set Framerate to Default as is the frame rate of your original clip, and it should stay like that.
• Choose your Custom Bitrate for less than 90 min video...

• ... or your CD Target size for full video.

• Select 2-pass encoding, it performs a slower but better compression - basically it makes sure you'll get a constant quality so you won't see blocks in fast motion scenes. Though it's disabled by default, is strongly recommend to use it except if you really care about time.

Subtitles

• Select Language subtitle (or None)
  

Picture Settings...

• Clik on Picture Settings... button to open edit window:
• You can re-size Width and Height keeping (or not) aspect ratio

You can scale down to width=512 x height=whatever handbrake says to improve H264 encoding speed and the quality is pretty well unaffected.

• Crop image to remove little black outline borders (we suggest use Auomatic button)

• Deinterlaced picture - only to use if movie has visible scanlines.

• You can Browse previous and next scene

• Useles OpenGL effects - play with the previous/next buttons after checking it, you'll see

Audio

• In Audio panel select first (and second language) and audio Sample rate (default 44100) and Bitrate (default 128).

• Click on Rip button to start encoding, a progress bar show encoding perc, fps speed and time remaining.

• Encoding can be paused, resumed or cancelled.
  

iPod Video settings

In Destination panel select:

• File format: MP4 file
• Codecs: AVC/H.264 Video / AAC Audio

In Video panel select:

• Encoder: x264 (Baseline profile)
• Quality: Average bitrate (kbps): 400

Note: enter also a value between 400 and 600; higer bitrate = higer quality = higer disk space.

• Select 2-pass encoding, it performs a slower but better compression.

In Audio panel select (as default):

• Sample rate (Hz): 44100
• Bitrate (kbps): 128

Clik on Picture Settings... button to open edit window and set size to:

• Width: 320

• Height: 240 (or less if aspect ratio is not 3:2) 

Note: Keep aspect ratio checked.
Calculate maximum video size using Podsize

iPod can play the following video formats:

• H.264 video
  File formats: .m4v, .mp4 and .mov
  Video: Up to 768 Kbps, 320 x 240 pixels, 30 frames per second, Baseline Profile up to Level 1.3
  Audio: AAC-LC up to 160 Kbps, 48 KHz, stereo audio
• MPEG-4 video
  File formats: .m4v, .mp4 and .mov
  Video: Up to 2.5 Mbps, 480 x 480 pixels, 30 frames per second, Simple Profile
  Audio: AAC-LC up to 160 Kbps, 48 KHz, stereo audio

Queue tasks

• Click on Enable queue check button.
• Click on Add to queue button to queue tasks.

• Click on Show queue to list queued tasks.
• Click on Remove button to remove task/s.

• Click on Start button to start rip tasks on queue.

How do I play files created by HandBrake

		VLC	MPlayer	QuickTime 6	QuickTime 7
MP4	MPEG-4 / AAC	Yes	Yes	Yes	Yes
	H.264 / AAC	Yes	Yes	No	Yes
AVI	MPEG-4 / MP3	Yes	Yes	No	No
	MPEG-4 / AC-3	Yes	Yes	No	No
	H.264 / MP3	Yes	Yes	No	No
	H.264 / AC-3	Yes	Yes	No	No
OGM	MPEG-4 / Vorbis	Yes	Yes	No	No
	MPEG-4 / MP3	Yes	Yes	No	No
Two language support		Yes	No (only 1st)	No (overlapped)

More info at HandBrake FAQ page.

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If you want to learn more about MPEG-4 and relish the idea of wading through technical speak, check out this thread
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Use WM9 today and get Micro$oft controlling the A/V market tomorrow for free.