Setup Assistant and Migration Assistant allow transferring either all apps, or no apps; you can't "pick and choose" individual ones to transfer or leave behind.

This is because many apps (we'll call them "complex apps" here) involve more than just the app in your Applications folder.  These apps come with their own Installers, and they put other files in other places, usually in your top-level /Library folder.   If those aren't transferred, too, the app won't work properly, if at all.

In addition, some may install "helper" apps.  Often those are named similar to the main app, but sometimes they have different names, and may actually be from a different maker.  Of course, these apps may have other files of their own!

These dependencies aren't registered anywhere when installed, so OSX has no reliable way of knowing which files and/or apps are associated with any particular app, so it would have no idea what else to transfer for any app you select.

So, if you elect to transfer apps, OSX transfers all apps in the top-level Applications folder (that don't already exist), and attempts to transfer all the "other" files.  The main sub-folders in the top-level /Library folder that may have selected contents transferred are: Application Support, LaunchAgents, LaunchDaemons, Preferences and PreferencePanes.  Of course, not all apps put files in all those places.

That process is very good, but not perfect.  Most apps will work fine, but a few, especially some of Adobe's, still won't transfer properly that way, as they put files in unusual places, and must be reinstalled from the original disc/installer.

In addition, a few paid apps may hide their purchase keys / serial numbers in unusual places, or be registered for a particular Mac or disk, so you may have to re-enter or re-register them.

2/25/13

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