Unfortunately, XDarwin preserves the sucky X11 clipboard mechanism. Which means that pasting is done with button3 (which Xdarwin frequently maps to command-click), and copying is an implicit part of selecting. So be careful with your selecting, or even manipulating windows; a jitter of a single pixel can blow away whatever had previously been on your clipboard.
That's actually the primary reason I haven't started using xterm in place of the differently-sucky Terminal.app.
