clipped from: notepad-plus.sourceforge.net   

• Backup your original Notepad.exe (we never know...).
• Copy notepad.exe which comes with this package into 4 directories (in given order) :
  1. c:\windows\servicepackfiles\i386
  2. c:\windows\system32\dllcache
  3. c:\windows\system32
  4. c:\windows
  When you replace notepad.exe in c:\windows\system32 and c:\windows, a "Windows File Protection" message box appears, click Cancel. Then another message box appears, click OK.
• Modify you registry (if you use installer to install your Notepad++, you don't need to do this step): Create key \HKEY_LOCAL_MACHINE\SOFTWARE\Notepad++, then add your Notepad++ full path as the default value of this key. In my case, it's C:\Program Files\Notepad++.