I just reinstalled my ubuntu distribution, and have to configure apache to serve perl pages outside of the cgi-bin directory, after a little bit of googling i found the solution.
You have to edit the /etc/apache2/apache2.conf and add to it the following lines.
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AddHandler cgi-script .cgi .pl
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<Files ~ "\.pl$">
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Options +ExecCGI
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</Files>
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<Files ~ "\.cgi$">
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Options +ExecCGI
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</Files>
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