Windows 3.1 really doesn't introduce anything new over Windows 3.0, but it is the first widely used version of Windows.

Most people ignored Windows 1.x and it's successor, Windows 2.x, and those that did pay attention usually only saw it as yet another graphical DOS shell. Windows came close to getting the axe as Microsoft's original intention was to replace Windows with OS/2. However, when that partnership fell through, Microsoft focused on producing their Windows NT product with the intention of using Windows 3.x to bring users to this new platform. Well, that lasted longer than they wanted, going through 95 and 98 as well before finally ending with ME.

There are in fact four different versions of Windows 3.1x:

• Windows 3.1: This version, seems to be the most common. Didn't include any networking software but could run on top of an existing DOS network stack.
• Windows 3.1 for Workgroups: Uncommon. Bundled Microsoft's Lan Manager networking software.
• Windows 3.11: Basically a service pack that patched a few things and bumped the version number.
• Windows 3.11 for Workgroups: Bundled a protected mode 386 network stack. Interestingly OEMs were still licensed to distribute it until November 2008.

This is the default Windows 3.1 desktop. Like Windows 3.0 it starts up with the Program Manager. The Program Manager is a major step above the old MS-DOS Executive from versions prior to 3.x, and the Executive that was previously bundled with Windows 3.0 as an optional shell is now no longer included with Windows.

The Program Manager, as well as it's companion the File Manager, is a Multiple Document Interface, or MDI, program. This enables it to display Program Groups in child windows instead of separate windows like in OS/2 1.x. Program groups as well as the icons inside them are usually added, removed or modified automatically when a program is installed or removed, however both can also be changed manually.
The other thing the Program Manager provides is big icons to click on, like the Macintosh has. That alone is a significant improvement over the MS-DOS Executive which just used lines of text that were clickable like invisible buttons or hyperlinks.

Program groups can be tiled as well as cascaded. The main window can also be maximized, however this will cover up any icons you have on the desktop.

Normal use of the Program Manager usually resulted in repeatedly opening and closing program groups. It usually became a sort of game to try and keep windows open but reszie and drag them out of the way to prevent covering up other program windows.
It is possible to create a custom program group and have all the important stuff fall in there, but this isn't always practical, especially when you have to set up thousands of PCs that aren't necessarily going to be used by you.

In practice it is usually just easier and faster to do things the DOS way and go to File>Run (or press Win+R) and type the program name.

The problems and weaknesses of the Program Manager inspired the creation of several alternate shells. Microsoft threw a wrench into that idea by forbidding OEMs from preloading alternate shells onto Windows 95 when it was released.