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.