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In olden days (say, 1995 or so), operating systems expected you to create your own organization for your hard drive. These days, the OS expects you to follow its rules. What are they? Why bother? Read on.
Modern operating systems, in particular OS X and Windows XP, maintain a "user profile" for each account on the computer. These profiles are separate from the applications on the computer (which are generally used by everyone who uses the computer), and contain the documents and settings unique to the user; this includes email, browser bookmarks, word processing documents, etc.
When IT provides you with a new computer, we will generally copy the user profile from the old computer, but not the applications or system files. If you haven't stored your documents in your profile, chances are you will lose them when we set up a new computer.
So where should you store files to make sure that they're part of your profile?
That's all there is to it--if you save your files there they'll be included when we transfer your profile. Files saved elsewhere (in the Applications folder, or root level of the hard drive, for instance) will not be included.