Ignacio,
Using AvgDev as signal and MRSNoise as noise (from the NoiseEvaluation script) will well account for different background levels.
As background level increases (due to changes in sky background, light pollution, air glow, etc) the ratio AvgDev/MRSNoise will decrease. This indicates a loss of SNR. The primary change is in MRSNoise, which increases due to the increased noise in the brighter background.
As sky transparency decreases (due to haze, fog, clouds, dust, air pollution, increased atmospheric extinction, etc) the ratio will also decrease. Basically fewer photons make it through the muck and so SNR decreases. The primary change is a smaller AvgDev, which effectively indicates a loss of "contrast" in the frame.
The ratio AvgDev/MSRNoise is relative and not absolute SNR. As I mentioned before, when you compare the ratios of the frames, the comparison is valid only for frames of the same target. Also, as I mentioned before, the comparison is invalid if the frames have wildly different light pollution gradients.
If you use this ratio to compare frames with different exposure times, the one with the longer exposure will be the one with the larger ratio (assuming everything else stays the same). Both AvgDev and MSRNoise individually will be larger, but the increase in AvgDev will dominate. This indicates that the longer exposure has the larger SNR of course.
Regarding color, only compare like colored frames to one another (e.g. red to red). The ratio is completely invalid if you compare frames with different filters. But for the same filter the result should be helpful. It will distinguish the better frames from the worse ones.
This technique is only a rough rule of thumb of course. It is nice because it requires neither optical nor sensor parameters.
If you need something more, check out the HST operating manual. There is a ton of stuff on accurate characterization and measurements procedures there.
Thanks,
Mike