Stored procedures offer several distinct advantages over embedding queries in your Graphical User Interface (GUI). Your first thought may be: "Why tolerate the added development overhead?" After seeing the advantages, you may change your mind.
Advantage 1: Stored procedures are modular. This is a good thing from a maintenance standpoint. When query trouble arises in your application, you would likely agree that it is much easier to troubleshoot a stored procedure than an embedded query buried within many lines of GUI code.
Advantage 2: Stored procedures are tunable. By having procedures that handle the database work for your interface, you eliminate the need to modify the GUI source code to improve a query's performance. Changes can be made to the stored procedures--in terms of join methods, differing tables, etc.--that are transparent to the front-end interface.
Advantage 3: Stored procedures abstract or separate server-side functions from the client-side. It is much easier to code a GUI application to call a procedure than to build a query through the GUI code.
Advantage 4: Stored procedures are usually written by database developers/administrators. Persons holding these roles are usually more experienced in writing efficient queries and SQL statements. This frees the GUI application developers to utilize their skills on the functional and graphical presentation pieces of the application. If you have your people performing the tasks to which they are best suited, then you will ultimately produce a better overall application.
In short, queries are best handled via stored procedures. While the initial development overhead is greater, you will more than make up for the investment down the line.