MyFinePix Studio, the software that came with the camera (which you can get on the Fujifilm website as well), is supposed to allow you to view and edit your movies but, to be honest, I could not get it to work on my HD movies (1280x720 16:9).
No worries because there is StereoMovie Maker that's available for free. After having installed StereoMovie Maker, you will probably be told that it cannot open any of your movies. It's because you don't have the motion jpeg (mjpg) codec installed on your computer. Google "motion jpeg codec" and you should be able to grab one, hopefully for free. Personally, I am using "motion jpeg codec 3.2.4" from free-codecs.com but I have the bad feeling it's just a demo. There's also a mjpg codec from morgan-multimedia.com but that one is definitely a demo.
Update on mjpeg codecs: forget about all those demo mjpeg codecs! All you need is ffdshow. A big thanks to David Kesner of the fuji3d yahoo group and dddphotography. Install the ffdshow codec, open the "VFW configuration" screen, select the "Decoder" tab, select "Codecs" in the list on the left, search for the "MJPEG" format in the list on the right, and change its "Decoder" to "libavcodec". The ffdshow codec has been around for a while, is free, and is highly recommended for all kinds of video formats, not just mjpeg.
StereoMovie Maker is real easy to use and there's a pretty good html manual that comes with it so there's no need here to delve into what each button does.
StereoMovie Maker has very basic editing capabilities as it appears that it can trim a movie (actually, it doesn't cut anything, it just moves the start and/or end markers, meaning that it only trims when you save) but I don't think it can merge 2 movies together.
It's cool and all to view/edit your movie with StereoMovie Maker but it would be even nicer to put those movies on the web somewhere. That's where youtube comes in with its 3D capabilities (it's pretty recent). So, let's look at how to save movies for youtube and the whole uploading and setting up on youtube.
Before you save your movie, make sure to swap the frames so that the Right frame appears on the left and vice versa. It's because the default in youtube for side-by-side viewing is Right-Left (cross-eyed). Technically, you don't really have to switch frames but you have to remember to change the "stereoscopic video options" when editing your video, once it's uploaded (I think). Now, you're ready to save the movie you've just edited: use the "side-by-side" option, pick a video compressor (divx or xvid, for example), configure the compressor so that you have a nice balance between image quality and file size, and press ok.
You should be ready to upload to youtube now. It's just like any other video in terms of uploading but, in order for youtube to know it's actually a 3D video, you need to add yt3d:enable=true and yt3d:aspect=16:9 (if 16:9) to your tags in the video description. That's pretty much all there is to it. When you view the video you have just uploaded, there should be a 3D icon with a drop-down menu where you can choose how you want to view the video (anaglyph, parallel, cross-eyed, and more). There should also be a settings button right next to the 3D button in order to select the definition (remember that the Fujifilm Finepix Real 3D W3 digital camera can shoot movies in 16:9 high definition).
Video I took of backyard birds with my Fujifilm Real 3D W3 camera (featuring a nice stereo window violation). You probably have noticed that there's no 3D button in the embed player. That's because you need to press play in order for the 3D button to show up.