I am builing a mobile application inside of DreamWeaver using jquerymobile. I have the site open but when I go to the Site menu inside of DreamWeaver I have no option for Mobile Applications.
What you should be able to do is select:
Site -> Mobile Applications -> Configure Application Framework
But I have no option for Mobile Applications. It is not just greyed out, it is completely missing.
I'm assuming you're following a tutorial or something. Mobile Applications is no longer a standalone option under 'Site' in CS6 onwards. If you're on CS6, you wont find it.
Instead, define a regular site and use Phonegap Build Service to build your app.