When opening 2 files in emacs, how can I have them appear side-by-side?

The following (to add to your .emacs) makes the window splitting default result in side-by-side buffers (rather than one above the other):

(setq split-height-threshold nil) 
(setq split-width-threshold 0) 

This default will also apply when you run a command such as find-file-other-window (Ctrlx4f).

(On the other hand, to manually split your window to get two side-by-side buffers, consider this answer).

Here's a function that will change a pair of vertical windows to a pair of horizontal windows:

(defun 2-windows-vertical-to-horizontal ()
  (let ((buffers (mapcar 'window-buffer (window-list))))
    (when (= 2 (length buffers))
      (delete-other-windows)
      (set-window-buffer (split-window-horizontally) (cadr buffers)))))

To do this automatically on startup, add this function to emacs-startup-hook:

(add-hook 'emacs-startup-hook '2-windows-vertical-to-horizontal)