Emacs features a minor mode, mouse-avoidance-mode, which causes the mouse to move away from the Emacs point when the point gets too close. This can be really helpful if you're used to moving your mouse away from the cursor to avoid typing "underneath" the mouse. In your custom-set-variables section in ~/.emacs, add the appropriate elisp:

(custom-set-variables
 .
 .
 '(mouse-avoidance-mode (quote animate) nil (avoid))
 .
 .

The animation parameters of mouse-avoidance-mode can be customized with M-x customize.

If you use middle-clicking to paste into Emacs windows but don't like how the paste occurs at the click location and would rather paste at point, use this in your ~/.emacs:

(setq mouse-yank-at-point t)

Thanks to Kevin Turner for pointing this out.