I think it's best to keep as much information as possible embedded into the map itself. This way if someone happens upon the data absent supporting documentation, they always have a means to understand it's context.
In QGIS, it seems there is a "metadata" section in the map properties. Access it by:
right-click on the layer > properties > metadata
here you can give the map a title and "abstract". I would use this field to document all the items you mentioned, but specifically would include:
- data sources
- method used to compute the map
- additional information/references needed to understand the context of the map.
- MOST IMPORTANTLY: your name/contact information.
In GRASS, a comment is automatically added to every map that describes the method used to compute the output image. It's a start, but in general metadata is invaluable.