As I recall, there is not a nice easy way, but there's nothing to prevent you from adding queries to organizational subfolders in groups that you can move in and out of the main saved queries folder as you switch projects.
Can you afford $40 to not only organized your queries, but to have them run with a single click?
Go to http://www.automatication.com/index.php?id=12 And download the trial version of Multi-Find/Change for InDesign. Works with CS5.
Here's some of what Automatication says MFC can do:
Organize Find/Change Queries Into Sets
MFC allows you to organize Find/Change queries into Sets (lists). Easy to use, the user interface enables drag and drop of different types of Find/Change queries into Sets.
Execute Multiple Find/Change Queries
Rather than executing individual Find/Change queries, MFC gives you the ability to perform Multiple Find/Change queries in a single operation. As a safeguard, it supports undo “Change All” to undo all the changes or undo by individual Find/Change query.
This is the Find/Change control that Adobe should have put into ID. But now that it's available for such a reasonable price, I don't mind it's missing.
If the links provided earlier don't work for you, you can try this one:
And in this title:
on pp. 38-39 illustrates a really very simple script is described to chain GREp queries.
Try the links listed as they are tested. We have a free beta script, XStrings.