From Visual Studio (and other tools, but lets take Visual Studio as an exampl here), I've configured the diff integration to always append the /solo argument.
What this does is very nifty: it starts a new instance of Beyond Compare for each call (otherwise it will first look for an existing Beyond Compare instance open then a new compare/merge tab in the first instance it founds).
It comes in especially handy when you have multiple instances of Visual Studio open:
The net result of /solo is that if you press Esc or Alt-F4 to get out of Beyond Compare, you immediately return to the Visual Studio session you started the compare/merge from.
Without /solo you will not return to Visual Studio (you need to find which instance of Visual Studio called it by pressing Alt-Tab, or moving over your task bar).
From the Beyond Compare docs at http://www.scootersoftware.com/help/command_line_reference.html
Command Line Switches
Note Linux users should prefix the switches with "-" instead of "/".
Switch Meaning /solo Forces a new instance of the program.