Thank you for the reply and the tutorials, they will always be handy. Perhaps I did not state my question clearly enough though. My inquiry was in regards to once I have created my video in After effects, what adobe product should I use to create a user friendly, cross platform format that I can embed into Adobe Muse? Short of posting the video to youtube and embedding the youtube video as an HTML snippet in a Muse Light box or equivalent.
You would render a lossless (or nearly lossless) file out of After Effects and use the Adobe Media Encoder to make your final compression.
I think using YouTube or Vimeo for your video is a much better idea than hosting it yourself. It will (most likely) load faster and it will save you a ton of bandwidth.
If you want to know what's best for Muse, I suggest asking on the Muse forum.
Michael's suggestion is a good one.