Is there a layer property box?  Where you can change the opacity?  Also, so you can hide and show the layer.

 What kind of layer are you thinking of?  If its a texture layer, you can hide it by unchecking it in the layer selection box and change opacity by adjusting the amount of color (or other properties) using the slider bars.  If its an object layer you can hide it by deselecting that layer, however you would have to change opacity by adjusting either z or ray transparency.

I'm trying to wrap my head around layers in Blender, and how they work.  I'm would like to make the scene with particles.  A teleport movie effect.  Something like,( beam me up Scotty), in Star Trek.
Here are some examples of what I would like to do:

www.youtube.com/watch

This is a nice effect, but I think they used a different application.

www.youtube.com/watch

This I like.  I do believe it can be done in Blender.

www.youtube.com/watch

This one seems to be simpler, I figured I would start with something like this.  The reason I was wondering about opacity in Blender.  I figured I would take the subject, and put him on his own layer.  Then reduce the opacity on that layer.  While at the same time, introducing particles on another layer.  I was thinking though, I also need a layer of the background.
 I seen something also done with masking.  Perhaps I should look into that.

Attached Link: http://wiki.blender.org/index.php/Manual/Compositing_Nodes

Blender layers aren't like photoshop layers--they're more for organizing your stuff than for compositing.  What you want is probably either a video editing program or the blender compositing nodes, which determine how things get rendered.

Thanks, that's what I was thinking, but I wasn't sure.  Thank you for linking me to the compositing nodes manual.
Inputs and outputs, I can understand.  With a bit of reading, maybe I can figure out what I can do.
Thank you again!  Peace