I am not sure what you mean by #1. Could you elaborate? Perhaps list a few applications like this?
As far as #2, it's just a folder with a special icon and a special name. If you create a folder "Applications" in your home directory it will get the same icon. But applications can reside anywhere. (Except in the Trash)
As for #3, there is no registry in OS X. It depends on the program, but generally moving applications around is perfectly OK. Again more specifics would help here.
As an example, take Apple's Remote Desktop program. This should be installed by an installer bundle (a "package file") because the program consists of more than just what's in the Application Bundle itself. There is software which needs to be installed under
/Library/ (and possibly
/System/Library, I an mot sure). However if you just copy the
Remote Desktop.app application bundle to a new computer, on first launch it will find the files are missing from their other locations and will copy them from within itself.
For another example, take the visrualization software VMWare Fusion. I haevn't tried their newest version, but version 2.0 can not just be copied from one system to another. being virtualization software, it requires kernel expensions to be installed under
/System/Library, as well as special device nodes created under
/dev and background processes to be running. This is all set up by the VMware install package and that is the only way to install it. Once installed the
VMWre Fusion.app application bundle can be placed in any folder on that mac -- but not copied to a new mac.
Oh and as one final point. There is no "registry" on OS X. System settings are stored in the NetInfo database which is vaguely similar, but vastly different. Application settings are generally stored in XML files called "plists" (short for property lists). The following will be interesting reading:
EDIT: You gave Starcraft as an example. Often games will store the Application bundle and the data rogether in one folder, so you'd have a "Starcraft" folder containing a "Data" folder and "Starcraft.app". In a case like this the application generally will work as long as the "Data" folder is kept at the same relative location. That is, is you move the whole "Starcraft" folder, you're fine, but if you just move the "Starcraft.App" file, you're in trouble. You might want to look into symlinks -- those can be useful if you're mving things around.