Gwyddion was recently moved from sci-misc to sci-visualization, that is to worse matching category (IMO, as a gwyddion dev). Please see http://gwyddion.net/features.php and ask yourself whether visualization is what the program is all about and whether it belongs between graph plotting tools. Unfortunately, nothing like sci-physics exists, therefore I propose to move it back, unless you plan to extinguish sci-misc, in that case I suggest to create sci-physics since all other major fields have their own sci subcategory.
I still stand by scientific visualisation as a more meaningful category than misc. I think a large part of it is visualisation and manipulation of images. This category is intended to be broader than just graph plotting packages. I also do not think the category is too important - people will still find it but I personally think SPM is in large part visualisation. The package categories are far from perfect and many applications belong to multiple categories and this relationship is not possible to convey with the current system. Stuff like qtiplot also does more than just plot graphs and it could be argued mathematics is a closer match by some.
