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Geoserver and Mapserver are both quite powerful but their developers pursued different goals.

To make the choice easier for you (I hope), here comes a general feature comparison:

Geoserver Mapserver
WMS both are good maybe a bit better [1]
WFS better, supports WFS-T [1] no WFS-T [1]
Technology J2EE [1] CGI [1]
Project start 2003 [1] 1996 [1]
Administration Web tool Mapfile generation can be aided by QGIS, but not comparable to Geoserver’s web admin tool
Extensibility good for Java developers [1] PHP Mapscript, good for PHP developers [1]
Cartography uses standardized SLDs powerful; styles are part of mapfile
Services one WMS/WFS/WCS service for all users [1] a mapfile means a service [1]
Querying CQL and OGC filters embedded SQL statements

New benchmarking results should be available soon [2]. Meanwhile, you might wanna watch last years results [3].

[1] http://osgeo-org.1803224.n2.nabble.com/Mapserver-vs-Geoserver-td4905798.html

[2] http://wiki.osgeo.org/wiki/Benchmarking_2010

[3] http://www.slideshare.net/gatewaygeomatics.com/wms-performance-shootout

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