Would questions asking for help performing a given task with a geosciences-specific software or library such as GPlates, PmagPy, PaSt or any stratigraphic tool such as RASC/CASC, CONOP9, UAGraph be on-topic in our new SE site?
I think that is a good idea. GIS of course has its own stackexchange site, but depending on the question, a GIS question could also be asked here. I would even allow very earth-science specific programming questions here, rather than on stackexchange proper. But it all depends on the question.
I think that questions about specialist computing techniques that are used for geosciences, in the abstract, should certainly be on topic.
I think that questions that end up as general computing advice, which could be better answered by Superuser, should be off-topic.
I think that in between these extremes there is a very wide ground of using specific software tools that are specific to geosciences, which should be mostly on-topic - but with a careful eye towards things drifting to Superuser territory. (and perhaps, as others have identified, a more lenient eye towards Stackoverflow, gis.SE, and things like the R and MATLAB proposals if they ever get off the ground)
I've just asked a question that I think falls somewhere between scenarios 1 & 3 above, which might or might not serve as a useful example :-)
Some other SE sites don't like questions regarding "resources" or "references," but I think that these WOULD be on topic. The purpose of the site is to study earth science, and a question that aids in this study, even if it is about study "resources," is worth encouraging.
I think that's a really good idea. I'm trying to use mailing lists for a couple of open source geophysical software packages, but the interest is usually low. A vibrant community like this would be better to find solutions. Moreover, people that don't use the software yet get an idea of what it can do and what kind of challenges to expect. One can always send a copy of the question and best answer to the mailing lists, if the moderators wish so.
I'll try Earth SE next time I get a SU or Madagascar related problem.