Well, in my (admittedly limited) experience, that is actually one of the weaker points of many open source GIS programs. Take for example GRASS or SAGA GIS. Both are very powerful analytical tools, but at the same time options to create nice looking maps from the results of your analyses are fairly limited. From the open source software I have tried, QGIS offers the best options to produce nice maps for printing. It is not yet on par with ArcGIS in terms of ease of use and results, but almost every release brings improvements over previous versions. And what I really like about it is that you can easily combine data layers from very different sources, e.g, raster and vector layers from a GRASS database with shapefiles and geotiff or ascii raster files.
And now with the Quantumnik plugin you can generate mapnik xml mapfile from an existing project, which can then be used in Mapnik. Mapnik is , to quote their website, “a free Toolkit for developing mapping applications. Above all Mapnik is about making beautiful maps”. I haven’t tried it out yet, but see this blog for more information. It sounds like a promising option and I will definitely try this out next time I have to make some printed maps.