We are doing this for quite some time already. We use 2 Canon 5D MarkII on a selfmade rig for Stereo filming, due to their big chip and full HD they deliver an awesome quality, also you are able to get the two lenses almost to eye seperation distance delivering very good results. The remote control is connected to both cameras, so you can control both simultaniously.
And I would recommend to use a parallel axis setup rather than a toe-in setup. It is much easier to composite afterwards, because in CG its much easier to handle parallel setups than toe-in.
The only reasons why there are stereo3d cams is to have 1 chip record the footage to ensure absolute color truth. With 2 cameras the colors between them can be off a tad.
But IMO the price for a stereosystem does not justify that. You’re better off buying 2 cameras, be it film or photocameras of the same type, you should just ensure they support a remote control, so you can control them simultaniously, I doubt any cameraman is good enough to handle 2 zooms manually and run them synchronous =)
If you got a Nvidia Quadro and Adobe AE or Premiere, there are plugins to display the footage on a stereo display during editing already.
The most common format actually is side by side and should work on most devices.
In 1080p it would be one video file with 3840*1080 where the 2 frames are side by side. If the device is set to stereo it uses the left frame for the left eye and the right frame for the right eye, but you can also watch it “mono”, then the right frame is simply cropped off.
Some devices also support to simply have 2 video files, usually the files have a suffix of _R _L or _right _left, and if you load one of the files, the second one is loaded automatically for the other eye (that’s what most PC video players use)
There are a few other options like one frame on top one at the bottom, or using every even frame for one eye and every odd for the other eye… It really depends on what your particular device supports.
But as I said, side-by-side is the most common and is widely supported. It’s best to keep the two files from the cams at all times, this way you can just re-render it into any desired format with the videoeditor of your choise.