Newbie Emacs tip: One way to set the background and foreground colors for an Emacs window is with the set-background-color and set-foreground-color commands:

(set-background-color "#003344")
(set-foreground-color "white")

These colors are my favorites, and look great on Emacs running in its own window. Unfortunately, if I run Emacs in a terminal window with this configuration, the nice dark green background gets rendered as ugly bright green. So I use conditional logic in my .emacs file to only set these colors when running in its own window:

(when window-system
  (set-background-color "#003344")
  (set-foreground-color "white"))

However, set-background-color does not set the default color to be used by new windows (new "frames" in Emacs jargon), such as one opened when you type M-x 5 2. This does not appear to be true for functions that adjust faces directly, such as with set-face-foreground, or with Emacs's Customize feature. One way to set the background color for default frames is as follows:

(add-to-list 'default-frame-alist '(background-color . "#003344"))

With this in your .emacs file, the explicit set-background-color et al. do not appear to be necessary. So:

(when window-system
  (add-to-list 'default-frame-alist '(background-color . "#003344"))
  (add-to-list 'default-frame-alist '(foreground-color . "white")))

From this, it appears set-background-color et al are not meant to be used to set defaults, only change the current frame's settings. Good to know.

P.S. I also use (set-cursor-color "red"), or rather, (add-to-list 'default-frame-alist '(cursor-color . "red")), on the dark green background.