I'm not sure about exclusive fullscreen, I'll have to look into it.
The circles are a result of how the stereogram's layers are calculated. Any given pixel will have a separation value, which rounds to the nearest integer. The separation value determines how far away it'll appear, but because of the rounding, things only appear in layers. Since the player position is represented as a point in space, you can imagine spheres around that point for each of the layer distances. So if the sphere intersects with a wall, the closer layer will look like a circle popping out of the wall. Like catalystman said, there's probably a way to get enough layers that it looks like true 3d; I just haven't figured it out yet.
Enemy tinting would be very helpful; I've been thinking about ways to do that without them being visible in the 2D "out of focus" view.
I could add a normal-view toggle pretty easily, but as it is now it would look like a depth map instead of the textured game. Still, that could be helpful.
I also have some more settings for controlling the noise, but I haven't added them all to the menu yet. I'll probably just add more settings so people can play around with them.
Thanks for all the feedback, I really appreciate it!