Update: JW7 is now available. Check it out here.
HLS is a powerful streaming protocol that Apple introduced in order to allow for live streaming on iOS devices. JW Player introduced HLS support in Flash too.
If you are looking to encode only a couple of videos, you could consider converting all videos manually, but if you have a larger library, it is important to replace any manual steps with a good encoding pipeline. Amazon’s Elastic transcoder has all the important components you need to create a transcoding pipeline using Amazon’s API’s.