How to hide desktop.ini files without hiding other hidden files/folders?

Found a better answer on technet:

Simple: click the "hide" box only in Desktop folder

(In Windows Classic view,) go to Windows Explorer; click on Desktop. Go to Tools/Folder Options. Click View, and check "Hide protected operating system files" - but, DO NOT CLICK "APPLY TO ALL FOLDERS". Just click OK. Now, only the Desktop folder will hide the files but they will still show up in all other folders.

Desktop.ini files by default have the System and Hidden attributes set. If you have Show hidden files, folders, and drives turned on, make sure Hide protected operating system files is checked under Windows Explorer's Folder Options / View tab:

I once used command prompt to hide some files and folders by changing the attributes.

Suppose you want to hide the file “desktop.ini” which is in your X: drive(can be redirected to any location). So open command prompt typing “cmd” in the “run” from Windows start menu.Now change the drive typing “ X: ” and then press enter.

Now enter the following command:

X:> attrib desktop.ini +s +h

(for hiding file/folder filename, replace 'desktop.ini' by filename)

Now desktop.ini would not show even if you display all hidden files in windows explorer.

To revert the process, following command needs to be used:

X:> attrib desktop.ini -s -h

This works fine in Windows XP, Vista, 7.

Resources:- [1] http://www.techtipsgeek.com/hide-files-folders-command-prompt-windows-xp/1001/