Command-Z: Undo the previous command. You can then press Shift-Command-Z to Redo, reversing the undo command. In some apps, you can undo and redo multiple commands.
Command-M: Minimise the front window to the Dock. To minimise all windows of the front app, press Option-Command-M.
Command-O: Open the selected item, or open a dialogue to select a file to open.
Command-S: Save the current document.
Command-T: Open a new tab.
Command-W: Close the front window. To close all windows of the app, press Option-Command-W.
Control-Command-F: Use the app in full screen, if supported by the app.
Command-Comma (,): Open preferences for the front app.