Right now, there several ways you can make 3D movies. Essentially, 3D movies are two channels of video combined into one with each channel filtered out red from the right and blue and green from the left.
Ron and AmyJo Proctor has a great tutorial on how to make 3D movies using 2 portable camcorders and Adobe Premier to overlap/filter the videos:
We started with two full color video channels (right and left) — anaglyph (the red/blue method) is not ideal, but it is accessible because you don’t need a special screen (just special glasses). We’d like to try this with polarization or autostereo some time.
For the anaglyph version, we overlaid the two tracks in a video editor and set the compositing mode to “screen” (also known as “add” in some editors). We removed the red channel from the right, then we removed the blue and green channels from the left.
We also had to adjust the offset a little bit so the “focus” was on one of the middle birds. Whatever the two channels “line up” on will be the “focus,” also known as the “screen plane depth.” Whatever is in front of that will “pop out” and whatever is behind will “pop in.”
The video editor we used was Adobe Premiere CS4, but you can also do this in cheaper / free software. We tried it in the video sequence editor in Blender (free at blender.org) and got a favorable result.
Another great way to make 3D movies is to use a hardware 3D converter such as the Nvidia GeForce 3D Vision Kit, which will allow you to play 3D games/movies on your 1080P HDTV easily.
PopularMechanics also has an article on using a Samsung 3D kit to play 3D games on HDTV, you can see here.
I think 3D HDTVs will be everywhere in about 2 years but if you want to get 3D right now, I think your best bet is with a 3D kit for your HDTV. That way, you won’t have to worry about converting anything.
Also, see how to convert any 2D movies to 3D.