Whitespace at the end of lines is farily annoying, and wastes space. It also generally annoys other developers if you send patches that introduce white space.
Luckily, emacs can show you with big red blocks where you've left whitespace behind. I think everyone (who hasn't already :) should add something like
(mapc (lambda (hook) (add-hook hook (lambda () (setq show-trailing-whitespace t)))) '(text-mode-hook c-mode-hook emacs-lisp-mode-hook java-mode-hook python-mode-hook shell-script-mode-hook))
to their .emacs file right now.