Currently (as of trunk), terminator treats mouse events in such manner that:
1. Ctrl + left click on an URL opens it, but the event is not consumed.
2. Middle click pastes the clipboard, and the event is consumed.
3. Rightclick opens the context menu, and the event is consumed.
4. All other events are not consumed.
Behaviour 1 is slightly problematic because the meaning of the event is ambiguous, and will trigger the hook (if existing) set by the program running inside the terminal (as well as open the URL if recognised by the terminal). The best way to avoid this is to consume the event if terminator decides to open the URL, since mouse events with keyboard modifiers (like ctrl + left click) are, though supported by ncurses and perhaps others, rarely used AFAIK.
Behaviour 3 is very troublesome because this disrupts console programs that support right clicks, for example w3m. The best way to avoid this is to instead use ctrl + right click for context menu (and consume the event), which is also the practice of xterm. This blocks console programs from accessing ctrl + right click events inside terminator, but should not quite affect the overall situation since the event should be rarely used by console programs.
Attached is the patch, which modifies the behaviours in the proposed way.
BTW, it might be slightly better to add an option to enable/disable the forementioned behaviours, but I am too lazy to do that :P
I'm very unlikely to apply this. This significantly changes a fundamental existing behaviour for everybody, to please the relatively small number of people using w3m. Further, Terminator tends to follow gnome-terminal as much as is practical, and gnome-terminal also has an un-modified right-click popup menu.
The only way this would be accepted is if it came as an advanced on/off setting which by default is not active.