I used to do it when I rendered the video in Adobe Premiere. But I have since switched to Sorenson Squeeze.
As for waternmarking, I use VideoCharge. It is a sweet program, and can do much more than cutting clips into pieces in seconds, as well as watermarking in no time.
Well worth the cost.
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Enough Said. 
"Would you rather live like a king for a year or like a prince forever?"
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