Most commercial tools do a good job at extracting the substrate parasitics from the completed layout; however, there are a variety of noise coupling mechanisms involving besides the substrate also the chip power grid and signal interconnects, pins, package, package-PCB interface, and PCB. Depending on the specific application, the substrate coupling may not be the dominant mechanism, and in these cases using a very accurate substrate extraction tool will actually give results far from what it will happen in the fabricated chip.
Bottom line is that a tool is only a tool and the applicability and limitations need to be decided only after understanding the noise coupling mechanisms in that particular application.
Another simulation tool is ChipQuake, developed by NoiseCoupling.com. This is a simple tool that estimates the noise coupling on the chip+package+PCB in the prelayout stages of the design flow. A fully functional free version comes with a noise coupling book also published by NoiseCoupling.com. That book has a very detailed presentation (three chapters) of the noise coupling mechanisms on the combined chip/package/PCB structure. More details about the ChipQuake tool, datasheet download, and book description and sample sections can be found at the NoiseCoupling.com web site
www.noisecoupling.comci