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Windows Media Encoder 9 Series is a powerful tool for content producers who want to capture audio and video content using the many innovations in Windows Media 9 Series including high-quality multichannel sound, high-definition video quality, support for mixed-mode voice and music content, and more. Choose from 32-bit and 64-bit versions of the encoder.
Source: http://www.microsoft.com/windows/windowsme...er/default.aspx

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Comparing 32-bit and 64-bit Versions
You can encode audio and video content in Windows Media Video (WMV) format using either the 32-bit version or the 64-bit version of Windows Media Encoder 9 Series. The version you choose will depend on your encoding scenarios.

The new Windows Media Encoder 9 Series x64 Edition contains the same feature set as the widely used 32-bit version of Windows Media Encoder 9 Series as well as the following updates:
VC-1 video codec. Windows Media Encoder 9 Series x64 Edition includes support for a fully SMPTE-conformant version of the new VC-1 video codec. Windows Media Video 9 Advanced Profile is part of Microsoft’s implementation of VC-1, which is the proposed SMPTE standard that delivers high-definition quality with highly efficient compression rates. It requires less computational power and can be decoded at full 1080i/p resolution on a typical computer. Windows Media Video 9 Advanced Profile delivers high definition (HD) content at bit rates as low as 6 Mbps to 8 Mbps.
Windows Media Digital Rights Management (DRM). In contrast to the 32-bit version of Windows Media Encoder 9 Series, the 64-bit version includes a separate DRM Protect Utility that allows you to apply DRM protection to your content files after the encoding process is completed. The DRM Protect Utility uses the information in the DRM profile you select to encrypt your content with a key, and other digital rights management settings that are specific to that DRM profile.
The DRM Protect Utility is available only for the 64-bit version of the encoder and cannot be used with the 32-bit version. Additionally, the DRM encryption functionality in the 32-bit version of the encoder does not work with the 64-bit version.


Encoding Scenarios
Windows Media Encoder 9 Series x64 Edition is designed to introduce you to the x64 support found in Microsoft Windows Vista. Therefore, some encoding scenarios are not yet fully optimized for the 64-bit version of the encoder. You should determine whether to use the 32-bit or 64-bit version depending on your encoding scenario and on your plans to migrate to x64 versions of encoding applications.

Scenarios that are optimized for the 64-bit version include:
Encoding 720p HD 2-pass PVBR content on quad-processor and dual-processor computers.
Encoding 720p HD AVI using the new VC-1 codec on quad-processor and dual-processor computers.

Scenarios that are not yet fully optimized for the 64-bit version include:
Resizing content from AP HD to AP standard definition (SD).
Encoding high-quality SD content.
source:http://www.microsoft.com/windows/windowsmedia/9series/encoder/versions.aspx