Use an environment variable to point to an "Open With" program

reg add "HKCR\Applications\myapp.exe\shell\open\command" /ve /t REG_EXPAND_SZ /d "\"^%MYAPPSDIR^%\myapp.exe\" \"^%1\"" /f

Note:

• to avoid expanding %MYAPPSDIR% by command line interpreter, % percent character should be escaped by the standard CLI escape character (^ caret): ^%MYAPPSDIR^%;
• to include a quote mark " in the data, prefix it with the reg escape character (\ backslash). E.g. \" here is a quote as the REG command will interpret \ as an escape for the character that immediately follows it.

An example (copy&paste from my administrator command line):

C:\Windows\system32>reg query "HKCR\Applications\mspaint.exe\shell\edit\command" /ve

HKEY_CLASSES_ROOT\Applications\mspaint.exe\shell\edit\command
    (Default)    REG_EXPAND_SZ    "%systemroot%\system32\mspaint.exe" "%1"

C:\Windows\system32>reg add "HKCR\Applications\mspaint.exe\shell\edit\command" /ve /t
 REG_EXPAND_SZ /d "\"^%systemroot^%\system32\mspaint.exe\" \"^%1\"" /f
The operation completed successfully.

C:\Windows\system32>reg query "HKCR\Applications\mspaint.exe\shell\edit\command" /ve

HKEY_CLASSES_ROOT\Applications\mspaint.exe\shell\edit\command
    (Default)    REG_EXPAND_SZ    "%systemroot%\system32\mspaint.exe" "%1"