I think that the ability to export to FLV was introduced in After Effects 7.
Mylenium, please elaborate especially about "Flash and creating a transparent player ." If my client simply wants to walk onto the screen from the right edge of the page, talk, then fade out or walk out, what else should I consider other than shooting on green screen, creating an alpha and preserving the alpha when exporting to FLV or SWF? Certainly HTML and/or XML code, but what specifically about the "transparent player?" Keep in mind, I'm the video producer, not the webmaster. Certainly, I'll consult with the webmaster about his/her needs. I just want to be sure I can properly produce the FLV or SWF with an alpha.
When your web person inserts the resulting SWF into the web page, they can set the window mode to "wmode = transparent" which will allow the web page to show through.
Depending on what version of Flash you're using, you can maintain the alpha channels. What version of Flash are you using?
I don't own Flash. I have AE 6.5, so I'll have to upgrade or buy Flash or some other software solution.
Assuming that your web guy has a relatively recent version of Flash, you don't need to export out of After Effects as FLV or SWF. Flash can convert other movie file types to FLV. You just need to use a format that supports alpha. I'd suggest using QuickTime or a PNG sequence.
That said, it is more convenient if you supply an FLV. After Effects 6.5 can't do that unless you have a version of Flash installed on the system, in which case you can use the QuickTime native exporters listed under File > Export. Use the "Flash Video (FLV)" option, and go into the Advanced Settings to enble Encode Alpha Channel. I suppose you could also use AE's File > Export > SWF option, but combining or overlaying SWF's is beyond my knowledge.
One word of advice for your web guy- if the video piece is very long (time) and/or very large (dimensions), or if you have multiple video pieces: avoid embedding it in the SWF. Set the SWF to link to it from the server instead. Flash tends to get grumpy (read: slow and crashy) if you try to embed a large amount of video data. It's also more efficient on the browser/Flash Player side to link to the video. But hopefully your web guy knows this already.
If you plan to upgrade, After Effects CS4 has native FLV encoding from the Render Queue.