In Word for Windows, there's a preference setting where you can choose the format of the clipboard contents when you copy an OMML equation (OMML = Office Math Markup Language; i.e., the "new" equation editor). You can choose between MathML and "Linear Format". Based on the way you phrased your question, I assume you know this already (but others may not).
You have the same options in Word 2011 for Mac; you just access it in a different way, but in a way consistent with Mac OS preference settings.
- In Word 2011, choose Preferences from the Word menu. In the Authoring and Proofing Tools section, choose Equations.
- In the Equations Preferences dialog, the When copying an equation section gives you this choice. (Copy linear format is the default.)
You mention Mathematica, and that's a good example, because using this technique you can copy from Word and paste directly into Mathematica as MathML, which Mathematica understands and can deal with. Most software applications and websites do not understand MathML, but MathType does. If you copy from Word 2011 in this way, then paste it into MathType, you can then use the equation in any of 700+ applications and websites that MathType works with.