JChemPaint is currently designed for linux, and possibly windows. On the mac, it does not conform to application conventions.
If there is a way to get it to do so for mac, and if that is a desirable thing (I certainly think so) then it needs to:
1) Use the proper shortcut modifier : it's not Ctrl, but the apple key.
2) Use standard shortcuts - Apple-W for close window, Apple-S for save, etc.
3) Closing the last window should probably not close the application. This could be a preference option.
4) Have a single top level menu, instead of a menu for each frame.
Obviously this is a kind of wish list, and in no way vital, but these are the osx style guidelines, and users come to expect programs on the mac (even java programs) to play by these rules.
I will be happy to implement/test/fix these things if they are seen as an okay possibility...