I have seen a couple of questions about this on the OneNote discussion group, so I decided I should post a comprehensive explanation.
This refers to OneNote 2007 page templates (used to be called "stationery" in OneNote 2003).
Summary: It is possible to reorganize the custom templates that you create and also the templates that you download off Office Online. You can reorganize the templates into your own groups.
This is actually just a special section file that is stored in this directory:
C:\Documents and Settings\%username%\Application Data\Microsoft\Templates
I say "special" because for every page there is also a hidden template name property that got put in there when you saved the page as a template. This name is used in the Templates pane.
When you download templates from Office Online they also go into the same folder, and appear as another bold group in the Templates pane.
When the notebook opens you will see "My Templates" as a section, along with any other sections corresponding to the templates you downloaded from the web.
Note: Don't forget to remove the empty pages from the Agendas and Personal sections.