Active stereo systems simulate stereopsis with a much more direct method than passive anaglyphs. Instead of relying on color information to separate the images to different eyes, most active stereo systems utilize glasses that can shutter each lens individually. The projector projects frames for each eye sequentially; the shutters on the glasses are synchronized to the projector so that the correct eye is shuttered for each frame. This synchronization occurs via an infrared signal that is transmitted from the computer's graphics card to the glasses.
In order to accomplish this the graphics card must be able to put out twice as many frames per second than under normal use. This requires a pretty advanced graphics card. It also needs to have an output for the infrared sync mechanism. There are only a handful of graphic cards that meet this description. Other disadvantages of the active stereo system is the amount of light that is let in through the glasses. Due to the nature of the shutter system you lose a great deal of brightness in the images. Optimally this winds up being less than 50% since the shutters are not completely opaque, but it is still significant. Another problem is the cost of the glasses. The most inexpensive pairs are around $200, the highest quality go for upwards of $500 a pop. The glasses themselves are also very fragile.