There are two types of menus in JCP: The main menu on top of the application and context menus which can be activated on elements (on many operating systems by a right mouse click). The content of the context menu depends on the type of element (atom, bond etc.) you click on.
As with buttons, there are menu items (in Atom and Bond menus) which change the mode (see Tutorial for an explanation of modes), others are one off actions (all menues except Atom and Bond). Many menu items share functionality with buttons, these have the same icon. Many of the actions on the context menus work on the specific element you clicked on (e. g. the particular atom), whereas the main menu always works on the whole content (or the current selection, if there is any). The following menus exist (note the wording of the menus is different if you are using a localized version of JChemPaint):