There was a question on the mono IRC about how to Copy&Paste from a Console window when running a console application from within MonoDevelop.
I tried to reproduce that, and first got the error:
cannot execute … File name has not been set
The answer is that you have to install the xterm package. See http://stackoverflow.com/questions/21834612/how-does-one-set-the-filename-in-monodevelop
Actually, here is the source that determines which terminal to use: https://github.com/mono/monodevelop/blob/master/main/src/addins/GnomePlatform/GnomePlatform.cs#L305
So it tries gnome-terminal, mate-terminal and konsole, depending on the environment variables for the desktop (GNOME_DESKTOP_SESSION_ID, MATE_DESKTOP_SESSION_ID, or KDE_SESSION_VERSION). If that fails, it falls back to xterm.
I am using XFCE4, and MonoDevelop falls back to xterm.
Copy&Paste in xterm works like this: just select the text, and then focus the application where you want to paste the text, and hit the middle mouse button. see also http://askubuntu.com/a/237947/194547