My Samsung TV can read every codec I've given it. You can grab the manual here:
http://www.samsung.com/us/support/downloads/UN40C7000WFXZA
Page 40 lists the available codec support.
Page 20 explains how the 3D feature works.
Your confusion about which codec to use might be because the content you produce (just like anaglyph content) is a 2D video. A "Side by Side" video, as played in VLC, will just look like 2 2D images playing next to each other - because that's all it is. People use mkvmerge to take the left eye and right eye and composite them together, literally next to each other. Unfortunately I have not found a simple to use tool that will convert between 3D formats - only tools that will stream.
Here's how it works from a customer's (me) perspective:
when I plug a USB stick in with a 3D mkv file
I start the Media Play feature
I browse to the movie I want and hit play
I pause the movie
I hit the 3D button on my remote control
The TV asks me which format the movie is in, either "Side by Side" or "Top-Bottom", or "2D -> 3D" (which is for 2D content).
I select the appropriate format, so far most content I've found is "Side by Side".
I put my glasses on.
I hit play (because I paused it before because turning on 3D takes a few moments).
Done.
If there's a way to inform the TV that the content is 3D, I have not yet found it. Although, the manual mentions this feature:
"3D Auto View (Off / On): If 3D Auto View is set to On, a “Side-by-Side” format HDMI signal with one of the resolutions below is automatically switched to 3D. Here, correct 3D information must be sent from the Standard HDMI 3D Format.
If a 3D failure occurs due to a 3D information error, set 3D Auto View to Off and manually select a 3D Mode using the 3D button or corresponding menu.
Support resolution (16:9 only)
1280 x 720p 60 Hz
1920 x 1080i 60 Hz
1920 x 1080p 24 / 30 / 60 Hz"
I'd be more than happy to help you test out your video files. You can email me. My slashdot username and my yahoo email account share the same handle.
I have a friend with the Nvidia setup and he can view pretty much all the 3D content that I've found. I have to use stereoscopic player, outputting a signal to my TV, in order to view other formats than the 2 I listed. And of course, Stereoscopic player will convert pretty much any format to any other format (except anaglyph formats can only be a target, not an input format).
Here's some sample 3D content you can compare with:
http://www.3dtv.at/Movies/Index_en.aspx
One caveat, I haven't actually tested that content on my TV. Most of it probably works fine, although some might be too high a resolution to support using Media Play - but I can play those from my Mac outputting over HDMI (but that's more annoying than Media Play).
Joseph Elwell.