I'm not so sure how compatible Apple TV is with a lot of video formats like MKV. I would go with Roku. Airplay from my experience is not the most reliable method of pushing content to your TV. (I think the Tested.com guys said the same thing too)
I would go for the Roku. It has a bunch of app like Giant Bomb, Plex, Netflix, HBO Go, Hulu, Spotify, Amazon Instant, Amazon MP3 streaming, and a bunch more. Seems like you are looking for a box to stream video files. I have been using Plex to stream my DVD collection and it's fantastic. I've used a lot of streaming software like TVersity, PS Media Server, Windows DLNA client and I always had problems with them connecting. Plex is the first program that has been problem free for me. Has transcoding so file compatibility should not be a problem and it auto tags you files with movie posters, directors, actors and stuff. One cool feature it has is when you select a TV show, the theme song will play while you browse the episodes. Plex also is a DLNA client so it will work on PS3 and 360 but the apps for Plex is a much better experience.
The Giant Bomb App is awesome too. You can sign it to get HD video and subscriber only content but you can't watch any live streams on it. I think you could watch GB live using the Justin TV app but that app is not good.
My two negatives for the Roku is the lack of a YouTube app. Luckily my Panasonic has a YouTube app built in so I can use that, but no YouTube on Roku really sucks. Also if you are a Comcast subscriber, you can't use HBO GO. You are the worst, comcast. If those 2 problems were fixed, I would probably buy another one for my other TV.
I don't know much about the WD TV except that it has no Plex app.
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