Queries are like reports, and I've noticed that over even a short time you tend to have dozens of queries stored in the module. This can cause some problems for the user though, as the grid is displaying only 10 queries at the time and you might not remember the right search terms to use the search.
In order to keep the situation manageable I think the best solution would be to have them stored in folders like documents and display them in the same folder tree.
This would allow you to store and access the reports that you need much faster. You could categorize them by the module from which the query originates from, and you could use even more granular folders if necessary.