If i have an animation that i know that it will be rendered with 80 samples and the quality is production ready with that. But i know also that there is one glossy / glass object, that will produce a lot of noise that will be enough good only with 500 samples or something like that. The question is: How do i render everything in that animation with 80 samples, except that one object with 500 samples?
Separate the objects with render layers and use samples override on the one that needs more samples.
Rendering with transparent background makes it easy to combine them back together in the compositor. Render properties -> film: transparent to enable that.
http://www.blenderartists.org/forum/showthread.php?305078-Render-elements-of-a-scene-separately-and-then-combine-them
I did that, but it seems that it takes very long time for the second layer to render the objects. Which is what i asked blender to do, but it also takes long to render those black areas in the layer that includes nothing? Is there way to prevent it from rendering those black areas and render only the objects i need?
If your glass object is the only mesh object in that Render Layer, and you have Transparent Background enabled, it should only be rendering the object, and not a black background. Is that what you’re seeing?
Now i have enabled that transparency in the render settings. But the problem is the same in second layer. Now the black areas of that layer is replaced with transparent areas. And Cycles takes very long to calculate those transparent areas of the image. I need it to skip those transparent areas and render only the objects that are in the layer.
If i create a render border. Or what is that thing you can do with Ctrl + b in camera view? It does it somehow in the way i need it to do, because there it calculates only that area that is selected. But render borders(?) cannot be animated. And the only reason why am i doing this, is to save some render time.
I am not sure if my previous messages were clear enough that actually none did understand my problem? Okay, here is an image to explain it. 
So I am trying to shorten my render time, but Blender uses very much time for doing some ridiculous task, rendering empty frame for few minutes? How to fix that?
The way i go about this if i need an animated renderborder… is creating 2 planes, which are parented to camera & fairly close to the camera (nothing should get closer to the camera then them)… and give htem a hold out material…
i then bump up the samples as needed and render off as png rgba… then composite the two images together.
I don’t know if someone did read my topic and then fastly created a tool for my needs, but here it is xD
Released only 9 days later. 
Is your glass object on a separate layer (regular layer, not render layer)? If not, then that might be the problem…Set the render layer with the glass object to only render the layer the glass object is on. However, I think this will prevent it from interacting with its surroundings (Shadows etc.)…
It is on separate layer and i think it works fine.
Do entirely separate renders, capturing each render output into separate file-sets, then explicitly join them in the compositor. Make sure that there’s nothing in the background, nothing in the world. If it’s taking time to render what you see as “empty,” it thinks there’s something there . . .
Is this method of separating out different elements to use different cycles settings viable for something like a volume scatter shader for the entire scene?
I ask because it seems that I need to use something like four times the number of samples for scenes that use volumic lighting than ones that don’t, however if I could limit those extra samples to just rendering the volumic lighting and nothing else, that might save a lot of time.