There are so many Linux distributions to choose from! What is the "best" linux flavor for a web hosting environment running primarily: Apache HTTP, Tomcat or JBoss, MySQL and Alfresco (not necessarily all in the same instance).
Are there any significant differences in terms of ease of administration and configuration, performance and stability for such applications, etc.?
What would you recommend?
They all use similar tools to administer things like webmin, and sshd.
What are you more familiar with. Red Hat based systems(fedora, mandriva) or Debian based systems(Ubuntu). This family divide will determine a few things. First rpm packaging vs deb packaging.
You also want to look at the level of activity of the project. Mandriva and Ubuntu are two examples of active distributions. That try to keep up with current releases of software.
Other than that most stuff performs with little difference.
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