Comparison of Open Source Desktop GIS Packages
There is a nice matrix (table) about "Matrix on OSGeo and COTS (Commercial off-the-shelf) software functionality", see this online spreadsheet. The effort of compiling the table was led by Tom McConnell, various project leads contributed to it.
I've now done a little searching myself on this and there seem to have been a few academic papers published with comparisons. Even the newest one is a year+ old now, but they do make for some interesting reading.
An overview on current free and open source desktop GIS developments (PDF) - Comprehensive comparison of GRASS 6.3.0, QGIS 0.9, uDig 1.1, gvSIG 1.1, SAGA 2.0.2, MapWindow 4.5, ILWIS 3.4, OpenJUMP 1.2D
Free and open source geographic information tools for landscape ecology (PDF) - A second paper (using the same material) with the same software and ArcGIS thrown in
Evaluating open source GIS for libraries (PDF) - Comparison of gvSIG 1.12, QGIS 1.0, uDig 1.1.1, OpenJUMP 1.2F, MapWindow 4.6.602, GRASS 6.4.0 (Via QGIS plugin)
Assessment of open source GIS software for water resources management in developing countries (PDF) - Started with just about every OS GIS ever conceived (over 30!) with a final detailed comparison of gvSIG, MapWindow, OpenJUMP and QGIS.
A bit meta, but someone's even written a paper on how to compare different GIS software; GIS software selection: a multi criteria decision making approach(PDF)
As I answered on the question you are referring, I did a comparison for several FOSS Desktop GIS in 2008, with the purpose of finding the system that fits a set of criteria. I also developed a framework for such selections, based on other frameworks. The paper is available under a creative commons license at: http://code.atlefren.net/download/dl.php?id=10