There are a number of other custom settings.  What follows is a brief description of each:

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Dolby Digital

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Automatic - Turbo.264 HD will select the best setting
On - Only available for the AppleTV and Custom Profiles
Off - Only available for the AppleTV and Custom Profile

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Chapter Markers

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These settings affect playback via QuickTime, like with an iPhone or Apple TV.

Automatic - Turbo.264 HD will select the best setting
On - Video will use chapter markers
Off - Video will not use chapter markers

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Closed Captions

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These settings affect playback via QuickTime, like with an iPhone or Apple TV.

Automatic - Turbo.264 HD will select the best setting
On - Captions will be on via QuickTime
Off - Captions will be off via QuickTime