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I stick this in my .emacs:
(setq x-select-enable-clipboard t)
(setq interprogram-paste-function 'x-cut-buffer-or-selection-value)
I subsequently have basically no problems cutting and pasting back and forth from anything in Emacs to any other X11 or Gnome application.
Bonus: to get these things to happen in Emacs without having to reload your whole .emacs, do C-x C-e with the cursor just after the close paren of each of those expressions in the .emacs buffer.
Good luck!
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.