Zivouhr, I did some conversions (for private viewing) a few years ago with a few of my anaglyph DVDs and yes, it does take ages. You have to split the film scene by scene and re-build it. I used StereoMovie Maker which allows you to save in side by side avi and you can save each side separately. You then have to colorize the black and white side and then you can add it to the 2D version. The results are quite good but the ripped 3D side is usually a lower quality and you can get embedded ghosting when compressing the file.
Fortunately, now that we have the Bluray 3D format, there is no need to do these laborious conversions any more.
Gae