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The Zune requires WMV3, and there is no open-source WMV3 encoder, so neither of those tools will create a WMV file that can be directly synced to the Zune - the Zune software will have to convert them first.
If you want to use WMV and convert them only once, then download Windows Media Encoder - it's free, and it supports WMV3 (a/k/a WMV 9).
However, those will both work for MP4/H.264, which can be synced directly without conversion.
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