I guess I can answer this question first hand Rares. I work for a small rural consultancy as an Environmental consultant. My role initially was simply to support applications for agricultural subsidy funding which is part funded by the EU and the UK government. However in order to do that we have to supply high quality maps, which in turn initially meant fairly high mapping costs from Ordnance survey the main U.K. supplier. As I became more proficient in the inhouse agri-specific GIS, I started to look at ways to improve our mapping. 

This led me to start using QGIS, source free data relevant to our work and in turn this led to a real change in the work that we started to contract for. While the UK is light years behind what you can source in the US for free, with a bit of imagination the information we can get transforms our output.

QGIS of course in not in reality free. It has cost me enormous amounts of personal time and my employers time to get me trained to a position where it is actually useful. My degree is in Environmental science and with a single GIS module in four years (in Esri!) I certainly didn't much in the way of background from my academic studies.

So your question is - what do we use then?. Well we accessed Land Cover data on Scotland from an academic institute in Aberdeen only because I asked for it, so the reality there is, not many even know it exists for free. We use forestry data extensively from the Forestry commission and Scottish Natural Heritage have a site called "natural spaces" with a considerable database for free. Ordnance survey (OS) offer a large database of free csv, shp and dtm's their "open source" website, however, much of the files lack detail and the only really useful element are maps at 1:10,000 scale that I then tie in with elevation data for moorland management plans.

We pretty much restrict our GIS mapping to incorporate wherever possible free data and this has cut our data bill by around 30% in the last years alone. 

In terms of academic papers it would be worth looking at Edinburgh university who have a world class GIS unit - hope that helps.