Hello Mike,

  Here is how I achieve my anaglyph images to decrease ghosting and preserve 3D effect. First, it is better to avoid black or white as a background. For example, in the render settings never selects black as the render background. Select a gray shader.

  As indicaed by Hairydekek, avoid red and cyan that are similar to the red and cyan of the glass filter. In this case, red or cyan in the image can remove the 3D effect because 3D effect depend on color separation. In fact, the Color Dubois anaglyph (see the Stereo Photo Maker menu) is an analglyph approach that change color to avoid this problem.

   So, in my images, I changed the red color of the T-shirt to orange. I used a gray background and I adjusted the brightness in Stereo Photo Maker. Here is how:

With your right and left image selected, in Stereo Photo Maker, select "Stereo" in the main bar, then "Color Anaglyph", then "Ghost reduced anaglyph". This selection will open the Anti-Ghost window. In upper part, first select the type of anaglyph. Half color is often a good choice. 

 Under the first histogram, move the upper arrow (brightness) to the left or right and look (with your anaglyph glass) at the image for the result (At first, move to the extreme to see the effect). Then move the lower arrow (contrast) to finalize if necessary. When finish, click on OK

 Now, when you save the stereo image, don't forget to check the case entitled "No compression ghosting". If you leave this case unchecked, some white lines will appear at the transition between red and cyan images.

 If you don't like the ghosting, learn the cross view method or purchase a carboard  stereoscope (Loreo Pixi 3D viewer ($2.50), see the link below and the image) for viewing parallel stereo pairs on computer screen.

http://www.berezin.com/3d/loreo_lite.htm