Created RunExit tool
A user at the VOGONS forums posted a question about being able to start Windows 3.1 (inside DOSBox) with another application and shutting down that Windows instance (and thus DOSBox) immediately when that application exits. This would normally be accomplished by setting the application as the shell in place of the default (Program Manager) by changing the shell=progman.exe line in SYSTEM.INI to the path of the application's executable.
Unforunately, the program in question refused to cooperate and threw an error message upon starting. Because of that, I created a simple utility using the ancient version 1 of Borland Delphi, as it was the only 16-bit version of Delphi, which is what was required to build a 16-bit program. The utility simply executes whatever file is specified as its first command line argument, waits for it to close and then silently shuts down Windows. For instance, starting it as runexit notepad would start Notepad and, after that closes, return to the DOS prompt. Since win.com itself accepts a command line of an application to start, it would be something like win c:\runexit\runexit notepad.
The tools itself and the Delphi 1 source code can be downloaded off the tools page.
Update (2013-05-25): New version adds support for setting the working directory and passing parameters.