Reg.exe in Vista has gain a new command line option "flags".  You can use it to see some interesting things, for example, whether a registry key is virtualized.

C:\>reg flags /?

REG FLAGS KeyName [QUERY |
                   SET [DONT_VIRTUALIZE] [DONT_SILENT_FAIL] [RECURSE_FLAG]]

  Keyname    "HKLM\Software"[\SubKey] (Restricted to these keys on
        local machine only).
    SubKey   The full name of a registry key under HKLM\Software.
  DONT_VIRTUALIZE DONT_SILENT_FAIL RECURSE_FLAG
    Used with SET; flags specified on the command line will be set,
        while those not specified will be cleared.

Examples:

  REG FLAGS HKLM\Software\MyCo\MyApp QUERY
    Displays the current flags of the key MyApp.

  REG FLAGS HKLM\Software\MyCo\MyApp SET DONT_VIRTUALIZE /s
    Sets the DONT_VIRTUALIZE flag (and clears DONT_SILENT_FAIL and
    RECURSE_FLAG) on MyApp and all its subkeys

C:\>reg flags "HKLM\SOFTWARE\Microsoft\Windows NT" query

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT
        REG_KEY_DONT_VIRTUALIZE: SET
        REG_KEY_DONT_SILENT_FAIL: CLEAR
        REG_KEY_RECURSE_FLAG: SET

The operation completed successfully.