There have been lots of comparisons done, just Goggle mapserver vs
geoserver.
IMHO the big differences are:
-Platform: C/C++ vs Java
-GeoServer WFS-T Support (although see TinyOWS for WFS-T and MapServer)
-GeoServer GUI-based configuration (vs mapfiles)
You may also be interested in the 2010 WMS shootout results :
http://2010.foss4g.org/wms_benchmarking.php See the link at the bottom
of that page to the PDF for results. That's one "neutral" comparison,
albeit for one aspect of things : WMS performance.
My 2 cents.
Yves
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