As Matt noted, the default and only Eclipse Navigator behavior that can be used in any perspective is to sort projects by name. My version of Eclipse (3.6.2) gives me the ability to sort resources by type, but this only applies to leaves of the tree (files).
But your question was about the PyDevs navigator, so I looked at the PyDev Package Explorer. I did not find a way to change the sorting of projects. My current installed version is 2.7.1.x, and as far as I remember, this applies to 2.6.0.x.
Thus, your question cannot be answered directly, because there is no way to change the sorting of projects without inserting the source code of the plug-ins or expanding the navigators (if there is a corresponding extension point).
Kai K.
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