The intention of this post is to document useful feature which you might not know or use yet. Of course the collection is a bit subjective... but feel free and invited to contribute and share your experiences.
It is possible to create other shapes than the standard cube or box. Simply select an alternative shape from the create-menu. You can chose between a sphere, cylinder, cone and pyramid. For a faster access, you can add those primitives to the "Quick Access Bar".
You can use the render-menu to create a rendered screenshot of your work. Click on the item labeled "Render" in the menu. If you chose to render an image (vs. turntable), you can define the section which should end up in your .png-file via a "Resolution Gate". Additional settings will allow you e.g. to define the background, add a watermark and specify the target path.
Display invisible matrices (Ghosting):
If you are in the edit mode of a matrix, it can be useful to see other matrices which are outside. To do so you can find an option "Ghosting" under the view-menu. Activate it and all matrices on your workbench will be displayed if you are in the edit mode.
If you have two matrices, it is possible to use boolean operations to either join both matrices into one, generate the intersection or to substract (difference) one matrix from the other. Together with the shapes mentioned above, this can be used as an easy way e.g. to give edges a round look.
Use "Modify > Other > Enlarge" if you want to multiply voxels, e.g. if you intend to have one voxel be represented by three voxels in a new matrix. "Modify > Transform > Scale" is only the second best option in such cases.
If you are encountering issues with the look of your (in another tool) imported .obj-files (created via Qubicle), check if you can find an option to "render the texture with linear interpolation", otherwise turn off the optimization within Qubicle and take it from there.