It might just be that perl is cross platform. In cases were you are using OS specific stuff like WIN32::OLE it is probaly habit.
One other use however is that some editors(VIM for one) will look at the name extension to choose syntax and if the extension does not tell it what Syntax to use, then it will reference the first few lines.
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Want more info? How to link
or How to display code and escape characters
are good places to start.