Ok... this is new to me, so I may not be entirely correct, but this is what I found while looking around:

In table MSysNavPaneGroupCategories, You can add different GroupCategories, so you could have multiple ways to group your objects.

So, in table MSysNavPaneGroups, GroupCategoryID is the [id] field from MSysNavPaneGroupCategories that you want to look at. Default for Custom is id=3

In the MSysNavPaneGroupToObjects, the GroupID field links to the ID field in MSysNavPaneGroups and the ObjectID links to the ID in MSysObjects.

Here is the query that I worked up to get the list of NavigationPane Groups...

SELECT MSysNavPaneGroupCategories.Name, MSysNavPaneGroups.Name, MSysObjects.Name
FROM (MSysNavPaneGroupToObjects INNER JOIN (MSysNavPaneGroups INNER JOIN MSysNavPaneGroupCategories ON MSysNavPaneGroups.GroupCategoryID = MSysNavPaneGroupCategories.Id) ON MSysNavPaneGroupToObjects.GroupID = MSysNavPaneGroups.Id) INNER JOIN MSysObjects ON MSysNavPaneGroupToObjects.ObjectID = MSysObjects.Id
WHERE (((MSysNavPaneGroupCategories.Id)=3))
ORDER BY MSysNavPaneGroupCategories.Position, MSysNavPaneGroups.Position, MSysNavPaneGroupToObjects.Position;

This is the first time I've looked at the Navigation pane, so I might have missed some things, but this looks like the navigation pane to me, so it works.

GComyn