I ALWAYS change the default to Alt = ALTernate (<-- hello?), Ctrl = Control, and Windows key(s) = Command. I just find the Win keys in PC keyboards to be a natural replacement for NeXT keyboard's Command key. Leave control as control, leave alt as alt. This weird control or alt as Command always felt awkward to me, especially now that keyboards have special GUI specific keys such as the Win key which is otherwise a hood ornament on systems GNUstep runs on other than Windows, such as Linux.
Also, when the Win key is unavailable (e.g. Ubuntu hardcoding it to desktop functionality), I use the Menu key.
Here's the contents of my NSGlobalDomain.plist:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "
http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>GSCommandKeyString</key>
<string></string>
<key>GSFileBrowserHideDotFiles</key>
<integer>0</integer>
<key>GSFirstAlternateKey</key>
<string>Alt_L</string>
<key>GSFirstCommandKey</key>
<string>NoSymbol</string>
<key>GSFirstControlKey</key>
<string>Control_L</string>
<key>GSFontAntiAlias</key>
<string>NO</string>
<key>GSModifiersAreKeys</key>
<integer>0</integer>
<key>GSSecondAlternateKey</key>
<string>Alt_R</string>
<key>GSSecondCommandKey</key>
<string>Menu</string>
<key>GSSecondControlKey</key>
<string>Control_R</string>
<key>GSTheme</key>
<string>NeXT.theme</string>
<key>GSWorkspaceApplication</key>
<string>WM</string>
<key>GSX11HandlesWindowDecorations</key>
<false/>
<key>NSBoldFont</key>
<string>Helvetica-Bold</string>
<key>NSFont</key>
<string>Helvetica</string>
<key>SystemBeep</key>
<string>/MondoLibrary/Sounds/Frog.wav</string>
</dict>
</plist>
As for UI settings I made a little preferences app, much more NeXT-like and inspired by Sergii Stoian's one for NeXTspace:
Here, you can see how I have only one Command key and it's set to the Menu key.
One thing I'd suggest we do is purge things like Meta and Super from our vocabulary. SUN is dead, and has been for decades. Fancy-shmancy terminals are a relic of a bygone era. Just about everyone has either a PC or a Mac. There are Win, Ctrl, and Alt for PC, and Option, Control and Command for Macs. Also Option = Alt and Ctrl = Control, so the only real "extra" or "new(-ish)" keys are the Win and sometimes present menu keys.That's what the everyday Joe Blow will call them, we should as well. It's just one of the many, many little things that hamper wide(r)-spread adoption.