newbie questions

... In addition, I use linux (Debian) and the desktop GIS tools that
I tried (svSig, Qgis, and some more) did not provide publication quality
maps.

I would strongly suggest you take another look at some of these
packages (especially QGIS).
These are relatively young projects, and are growing (changing)
quickly. For example, just
recently, some very advanced symbology enhancements have been made to
the QGIS project,
and will likely be available in the next release (due out next month).
Though of course, for graphs
and other statistical outputs, nothing beats R!

Carson

Carson J. Q. Farmer
National Centre for Geocomputation
John Hume Building,
National University of Ireland, Maynooth,
Maynooth, Co. Kildare, Ireland.
http://www.carsonfarmer.com