What I do is to use a good terminal tool (PuTTY on Windows, Konsole or Terminal on Linux) that has copy facilities built-in.
In PuTTY, you highlight the text you want with the mouse and then paste it elsewhere. Right-clicking in a PuTTY window pastes the contents of the Windows copy/paste buffer.
In Konsole or Terminal on Linux, you highlight what you want then press Shift+Ctrl+C for copy and Shift+Ctrl+V for paste.
In the win32 compile of emacs, yanking text does put it on the copy/paste buffer .. most of the time.
On Mac OS X, the Apple-key chortcuts work fine, because Terminal traps them.
There is no direct way of doing it on the commandline because the shell does not maintain a copy/paste buffer for each application. bash does maintain a copy/paste buffer for itself, and, by default, emacs ^k/^y shortcuts work.