First, open gnome-terminal (terminal) and then click edit, select prefrences and then disable the option "show menubar by default in new terminals". Close the prefrences menu, right-click anywhere on the output area and de-select the option "show menubar" before closing the terminal.
Now, open a new terminal, right-click anywhere on the output area and select "show menubar". The menu should now display properly in the top panel instead of the window like it did before.
Next, click "terminal" in the top menu, select "prefrences" and this time enable the option "show menubar by default in new terminals".
The menu should now display in the top menu instead of in the window from now on and the problem should be fixed.
(tested on a newly installed ubuntu-desktop 14.04)
If you didn't already give this a try, you may want to see if this command-line option works for those apps by disabling the integrated window menus for your user-profile using gsettings.
gsettings set com.canonical.Unity integrated-menus false
As far as indicator-appmenu is concerned, you can check to see if it's installed by typing the following command in an open terminal:
dpkg -l | grep indicator-appmenu
The output should list indicator-appmenu if it's installed which I'm sure it probably is but you never know, if not, you can install it or even reinstall it just for good measure like this.
sudo apt-get update && sudo apt-get install --reinstall indicator-appmenu