Emacs 24 has built-in theming, which doesn’t use statements like (require 'color-theme). As Drew points out in the comments, there are differences between color themes and custom themes, and the new direction is towards the latter. Try M-x customize-themes to take a look. From .emacs, you can do things like (load-theme 'wombat t).

But…

It may still be going wrong for you. One thing that can mess it up like this is changing the face — maybe in the custom-set-faces part of your .emacs file. Emacs’s interactive customization automatically includes the color information (both background and foreground) of whatever theme you happen to be using at the time you set it, so this can definitely make trouble with color themes. If that is what’s causing it, you can just set the particular attribute you care about with something like

(set-face-attribute 'default nil :height 120)

That will change the font size without changing the colors.