Basically, if you close one eye then thats the red image and you close the other then thats the blue image. Those two images are not just a lateral shift left and right becuase as Midgard says stuff in the far distance is the same for both eyes. What you have to do is shift close stuff more than far stuff. Only then does it look 3D with the red / blue glasses.
You can use cross polarizing glasses too but you need to find a source of image that can be made to go one polarization and then the other which is hard. IMAX type cinemas etc.
Another way is to use some special active glasses with LCD windows in them. They flash alternatively clear and black very fast and alternately for each eye. You can set up your monitor so that every second frame goes to each different eye. Then you draw your 3D scene with slightly different perspective for the two frames and chop them fast.
Theres another way without glasses too. You can get this plastic stuff that has a sawtooth pattern of clear ridges across. Often you see it on postcards or book covers and it gives the impression that the scene changes as you rotate the book cover. They usually do 2 or 3 frames of animation across the sheet. They do this by interleving the different images in vertical strips and the plastic seperates them again. You can stuff one of those sheets infront of your monitor and get the pixel spacing just right and then you can sit in just the right position and see it in 3D too.
Finally there are autostereograms. These are the pattern of random dots where you defocus your eyes by relaxing them - opposite of cross eyed - and then suddenly an image snaps into view and its 3D too. Harder to get that in color tho and about 20% of people just cant seem to do it and see the image.
If your prepared to get some wacky wacky hardware then theres more options. Holograms, rotating cones, lasers and special materials have the ability to get you a true 3D image though its hard and still pretty experimental. Actually the only common one I can think from that set is the holographic images on certain CD's like Microsoft OS'es or on credit cards and other security products like that. Theres a lot of research and development going on to try and create an animated hologram. Its very hard tho.
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