Check Your Data
What format does the data use? Did the author use standardized or ad hoc methods of formatting, such as the "new paragraph" command versus "Enter-newline-newline" in a document? Does the data include files such as images?
In some cases, the differences in format are really minor. For example, MySQL stores dates as YYYY-MM-DD, while Microsoft databases often use MM-DD-YYY.
If the formatting differences are extensive, one fruitful approach, especially with Microsoft Office–type documents, is to use an intermediate format that both the Windows and the open source application can handle. For example, Rich Text Format (RTF) files are standardized and well understood in both the Windows and open source worlds. Often you can avoid detailed conversion processes by using an intermediate format.