Welcome to Apple Support Communities
You have to transfer all applications. Note that if you are migrating from an older OS X version, the apps that came with Mac OS X won't be modified, as they are required by Mountain Lion. Apart from that, all the applications you installed yourself will be transferred.
(by the way, any one know how you can retrieve login details if you can't remember which email address you used? I have found old Communities posts of mine, but can't remember which email address I used, so can't post as the same person as I was before; had to set up a new account & ID)