Applications are what used to be called programs.  In principle, applications do not contain information; files (often referred to as documents) do, and they are manipulated and processed by applications.  Folders (known in the industrial computing world as 'catalogs' or 'directories') are containers for files or applications, whose structure is under the control of the computer user.  Treat them like virtual buckets. These make organization more convenient. Without them, you would have to stare at your complete list of files, and manipulate them singly.  Folders may exist within folders, giving you as many layers of filing as you wish.  Files are your own, and don't have to be stored in the application's folder.  You can store them in any convenient place, in a folder you can create for yourself.

Applications vary widely, but are always platform-specific.  There is no software which can be run on two different platforms, so you buy the application in a form suitable to the platform you use. Platform and application are locked together just as tightly as chip and platform.  An application might be used to view one or more files, which might be pictures (as with Photoshop), a letter (Microsoft Office), or play a sound (Performer) or a video (QuickTime).  In most cases, the application is primarily used to change those files (documents), for example to make a picture brighter, to add more words or to change some musical notes.  In some special cases, such as Web browsers, the application is simply for using and moving between large numbers of files such as make up a Web page.

An alias (of a file or application) is a clever and useful thing but often difficult to understand.  An alias mimics the properties of its 'original' file, but can be placed anywhere: on the desktop or in the folder of your choice.  When you move, copy or delete an alias, you do not affect the original file.  But when you double-click on the alias, you open the original file, wherever it might be.  You may collect aliases of files that have some common property, such as letters to one particular person selected from your 'Letters' folder, or selected photographs for presentation out of your collection filed in folders named after the date you took them.  You might create your own folder 'Applications Aliases'; from here you can open any application whose alias you have included, without the work of navigating to its specific folder.