Though OS X offers great multitasking features, having multiple windows open in multiple applications can sometimes hinder concentration. If you don't want to put the application you're mainly working with in full-screen mode, there are other options.
For example, you can minimize windows to the OS X Dock, but this has its limitations, including filling the Dock so it expands across your screen. Additionally, it requires you to click and expand the window from the Dock to preview its contents, which results in the documents being reordered in the Dock when you minimize it again.
If you're looking for other ways to keep multiple applications open, while reducing confusion, here are a few to try.
The first is the system's application-hiding feature, with which you can make the current application or other applications invisible while leaving window positions untouched. By mastering this feature you can make quick work of what is displayed onscreen.
The default options for application-hiding in OS X are to press Command-H to hide the current program, or to press Option-Command-H to hide all applications except the current one.
You can also do this by choosing these options from the Application menu (the first menu to the right of the Apple menu, which should be the name of the current application), or by right-clicking an open application's Dock icon and choosing the Hide option from the contextual menu.
Once hidden, not only will the program's windows will disappear, but any minimized windows for that program will also disappear from the Dock. The program's Dock icon will remain, but will become translucent to indicate it is hidden.
To unhide a program, simply activate it again by clicking its Dock icon, or by pressing Command-Tab to switch to it, and the hidden program will reappear alongside current programs.
A final neat tric: to hide the current program when switching to another one so the system jumps between them instead of showing them simultaneously, simply hold down the Option key when clicking a program's icon in the Dock.
Unfortunately this last shortcut is limited to the Dock or when launching programs from the Finder, so you can't use it with the system's Command-Tab feature or another hot key.
Rather than hiding applications, a second option is to make use of Mission Control and create different work spaces for your applications. While hiding applications has its conveniences, you cannot collect programs in groups to then hide or reveal; however, you can do something similar by sequestering programs for one workflow or project to a different desktop.
To do this, simply activate Mission Control by pressing F9 (you can set up a hot key or mouse action for this in the System Preferences). You can then create a new desktop by moving your mouse to the top right and clicking the indicator flag that appears. From here you can drag application windows from your first desktop to this new one, and then switch to them on a per-desktop basis instead of minimizing or hiding specific windows and applications.
A final tip about using Mission Control: there's a box in the Mission Control System Preferences to group windows by application. With this checked, in Mission Control you can move all the windows of one application to a new desktop by simply dragging the application icon (which will appear in front of its windows).