The short answer is that you can use them like you would use any other TEI file. You might render then into XHTML for display on the Web (the Web View function will create some basic files to get you started with this). You might store them in an XML database such as eXist. You might turn them into PDF files using XSLT, XSL:FO and a tool such as XEP or Apache FOP. As an example, we are currently working on a project to mark up 17th century French engravings, along with related polemical texts, using TEI P5, and we're storing the XML in eXist, querying it with XQuery, and rendering output using XSLT under Cocoon.
There are two answers to this: difficulty and expense. The IMT is written in Borland Delphi, one of the best RAD (Rapid Application Development) tools ever created. Delphi uses Object Pascal, which is not really portable from Windows. In addition, the tool uses a lot of other open-source Delphi libraries for graphics, Unicode and XML file handling. Our experience in doing parallel development in Delphi and Java (one choice for cross-platform) is that Java development takes two to three times as long, and when it comes to GUI development, it's notoriously difficult compared with Delphi. Another option would be to create a tool based on the Mozilla engine; we will be looking into that soon. For our purposes, though, (the projects for which we're building the tool), working on Windows is not a problem for our markup people.
However, the application is open-source, so there's nothing to stop you from porting it to another platform if you have the resources. If it becomes popular enough, we might be able to find those resources ourselves.
Please note that you can run the Image Markup Tool under Linux using Wine, and it is also possible to use it on OSX using a package created by Guenther Goerz. See Running the IMT on Linux and OSX for detailed instructions.
The "Web view" is a simple example of how you might create Web-based output from your markup project. When you click on File / Create Web view the program will create a set of output files for you:
The last two files are not required in order to make the Web view work; they're provided so that you can use them as a starting point for your own customizations, if you want to make changes to the HTML rendering through XSLT.
DocBook is another popular XML file format used primarily for documenting software and hardware. Because one of the projected uses of the Image Markup Tool is as part of a documentation system (as I've used it in the tool package itself, to document screenshots of the application), I've provided a basic XSLT-based import/export functionality which will create and read back DocBook files. This is currently rudimentary -- only a few TEI tags are converted to DocBook -- but I will be making this more sophisticated as time goes on.