In the BI renderer, which I normally use, you can capture multiple RenderLayers into a single MultiLayer OpenEXR file. So, you could use this facility to try to isolate the various sources of light.
However, I think it would be difficult in practice, because when you do have multiple lights “turned on” and contributing visual data to the scene, the effect of all of them on each illuminated object is naturally “cumulative.” When you’re compositing, you really want each separate track to be “pure, pristine, and distinct,” so that you can apply one set of operations to the entire input and get the desired outcome everywhere in the frame. Things like light and shadow can easily “add up” when you actually go to put the whole thing together.
I’d shoot multiple renders, each with a particular set of lights “turned on,” to be certain that each one captured only the lighting (and, separately, the shadow) effects from each source. Even though it seems to “take more time,” it really doesn’t. (Python scripts can be very helpful.)
This also has the advantage that, if you need to tweak one particular aspect of the light, you only need to re-render that aspect. If your only choice was to re-render everything, you’re really not saving time anymore. If you feel that you have to do it, because different sources influence one another, you don’t have a clean “comp plan.”
The reality is that, when you finally do get to “comp,” you will have to change some things. So, plan for that. Set up your scene, do the various rough lighting-shots, then sit down right away and do at least a rough comp. Look for problems: you will find them. Especially doubled lights and doubled shadows.