First of all, thanx for the comments and favs
And what I use for software. The anaglyphs I make are "real" anaglyphs. Meaning that I have 2 seperate shots for left and right. Just like you get when you use a 3D camera. But my 2 shots I made in program called Bryce. I make the render, move the camera in the program a little bit to the left and make the 2econd render.
Then in a program called AnaBuilder (freeware at http://anabuilder.free.fr/welcomeEN.html) I merge the 2 images together and then the anaglyph is finished.
If you use Photoshop to make "fake" anaglyph (meaning you have 1 photograph to manipulate it into anaglyph), then what I wrote can not be done by you because I use 2 images.