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AE supports H.264, but naturally this applies. Look up proper rendering procedures in the help otherwise. It seems you are looking in the wrong place and need to brush up on the basics. For all other formats simply render uncompressed and convert them in external tools. At this point, no Adobe app supports these non-standardized/ experimental formats.
You're certainly right about me needing the basics, as I don't have any experience using After Effects. I'm trying to learn the program now. I've been doing research to decide what I wanted to use to do some animation and wanted to make sure there wouldn't be an issue getting it into the right format. Thanks for the quick reply, I believe I already found a program to do the converting.
You're best bet is to go .mp4 for now and AE does support H.264 encoding. In fact CS4 is rather good at it. If you are using a Flash player then h.264 will cover all of your basic browsers. As far has HTML5 and WebM goes I would say to hold off, this is coming from experiance. HTML5 is not finalized yet and all of the browsers are implementing their own versions of it. So you end up having to make different files\formats for several different browsers anyway. Why not just contiune to use the Flash player and use .mp4s or .flvs for the time being? And to be honest .h264 looks better then WebM with all the tests we have currently done.
If you are worried about iPads\iPhones that's not really a big deal because they also support h.264.
AE won't output to WebM/VP8. that's the answer you're likely looking for. i presume you've moved on by now, but others are still looking for this answer.
as for H.264... the licensing crap that's coming up now is pushing it into the dirt. while the WebM/VP8 format is perhaps not yet as strong as H.264, you won't have the potential legal issues that H.264 will have.
so until Adobe or someone else comes up with an export module for AE, look to something else, like Sorenson Squeeze or Miro.