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.

Steps:

1. When you create the your custom templates, they go into the My Templates group in the Templates pane.

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.

2. You can open the Templates directory as a notebook and reorganize your stationery. To do this, click File > Open > Notebook and specify the path to the Templates directory.

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.

3. Create other sections that represent the groups that you want to have, e.g. Agendas, or Personal. Move the pages from the My Templates section to these new sections. You can just drag and drop.

Note: Don't forget to remove the empty pages from the Agendas and Personal sections.

4. When you are ready, close the notebook (File > Close this Notebook)

5. Restart OneNote and go to Templates pane. You should see your new groups in the pane.