7u6 b16 does not create:
HKCR\Applications\javaws.exe
HKLM\SOFTWARE\Classes\Applications\javaws.exe
7u6 b15 creates:
HKCR\Applications\javaws.exe\Shell\Open\Command
"C:\Program Files\Java\jre7\bin\javaws.exe" "%1"
HKLM\SOFTWARE\Classes\Applications\javaws.exe\Shell\Open\Command
"C:\Program Files\Java\jre7\bin\javaws.exe" "%1"
HKCR\Application\javaws.exe - we do not use that key anymore.

HKLM\Application\javaws.exe - I do not know about this key ?  There is not even HKLM\Applications in my machine. (checked win7 and xp)

We use the following for registering javaws and jnlp file types:

// key: HKEY_LOCAL_MACHINE\SOFTWARE\Classes\.jnlp
//     value name:  (Default)    value:  JNLPFile
//     value name:  Content Type value:  application/x-java-jnlp-file  (tell
//        browser to invoke us when something of this mime type is downloaded)
//
// key: HKEY_LOCAL_MACHINE\SOFTWARE\Classes\JNLPFile
//     value name:  EditFlags    value:  0x00010000 (OpenIsSafe) (Avoid warning
//        and invoking javaws to open arbitary files)
//
// key: HKEY_LOCAL_MACHINE\SOFTWARE\Classes\JNLPFile\Shell\Open
//     value name:  (Default)    value:  &Launch  (default action when JNLP file
//        is double clicked)
//
// key: HKEY_LOCAL_MACHINE\SOFTWARE\Classes\JNLPFile\Shell\Open\Command
//     value name:  (Default)    value:  "<path to javaws>" "<%1>"  (command
//        to launch when JNLP file is downloaded or double-clicked.  %1 will be
//        file path to JNLP file)

and there is also these keys still:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\App Paths\javaws.exe

Is there any functionality broken in javaws because of this bug ?
Corrected the second key - should be HKLM\Software\Classes\Applications\javaws.exe instead of HKLM\Application\javaws.exe. 
Not sure about functionality, noticed this issue during CR 7166335 verification.
Assume that HKLM\Software\Classes\Applications\javaws.exe is not used anymore too.
I will re-dispatch this issue if we notice some related broken functionality.