In Kirrkirr, you can make notes about any word, and have them attached to a dictionary entry. You can enter a note after clicking on the Notes tab. Or if you click the Keep button or select the see definition option in theNetwork popup menu for a node, you can get separate Formatted Entry and Notes windows that you can move around the screen.
You can change the colour of the notes from the default canary yellow by selecting the Options | Preferences menu item.: