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YouTube's website explains the best formats.
Read up. Do tests.
At any rate you don't want to use AE for your final render. Render lossless out of AE and then use the Adobe Media Encoder to compress it for the web. The Adobe Media Encoder can do multipass encoding which will give you a better quality video for a smaller file size. After Effects can't render out with multipass encoding.
You will find a few YouTube presets in the Adobe Media Encoder, for various formats, including Standard Def and High Def.
I usually use H.264 (mp4) format. And I think YouTube prefers H.2.64 that format because (as I understand it) it H.264 makes it easier for YouTube to stream different streams based on visitors' devices (someone please correct or clarify if I am not quite correct about this.)
Also, as you encode, keep in mind that YouTube has their 2 gigabyte limts.
Thanks for the advice.