There are many good ways to store application data (call it serialization).
Personally, I think for larger datasets, using an open format is much, much easier for debugging. If you go with XML, for example, you can store your data in an open form so that if you have file corruption issues (i.e. a client can't open your file for some reason), it's easier to find. If you have sensitive data in there, you can always encrypt it before writing it to file using key encryption. Microsoft, for instance, has gone from using a proprietary format to open xml in their office docs. They use .*x extension (.docx, .xlsx, etc). It's really just a compressed folder with xml files.
Using binary serialization is, of course, the industry standard at the moment for most standalone applications. Most likely that is because of the application framework they are using (such as MFC, which is old). If you take a look at most of the serialization techniques in modern application frameworks, XML serialization is very well supported.