Also higher end encoders such as Telestream Episode, the same people who make Flip4Mac.
Since December 2007, H.264 .mov has been compatible with Flash so you can export that and it will work fine. Some prefer H.264 .mp4 for Flash.
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en.wikipedia.org]
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On August 20, 2007, Adobe announced on its blog that with Update 3 of Flash Player 9, Flash Video will also support some parts of the MPEG-4 international standards.[11] Specifically, Flash Player will have support for video compressed in H.264 (MPEG-4 Part 10), audio compressed using AAC (MPEG-4 Part 3), the F4V, MP4 (MPEG-4 Part 14), M4V, M4A, 3GP and MOV multimedia container formats
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Adobe also announced that they will be gradually moving away from the FLV format to the standard ISO base media file format (MPEG-4 Part 12) owing to functional limits with the FLV structure when streaming H.264. The final release of the Flash Player supporting some parts of MPEG-4 standards had become available in Fall 2007.[12]