Question: How can I tell (from inside of .emacs) whether or not the Emacs version is Cocoa? I only want some configuration options to apply when they are loaded in Cocoa Emacs and not in the command-line version.

Answer: 
Try `(featurep 'ns)` to check for the NextStep emacs feature. See also `C-h v window-system`, can check if that variable is `'ns`.
It's sufficient to do something similar to the following:

To see if you're on a Mac and not running in the command-line version:

```
(when (and (eq system-type 'darwin) window-system)
  (setq my-option "cocoa"))

```

To see if you're on a Mac and are running in the command-line version:

```
(when (and (eq system-type 'darwin) (not window-system))
  (setq my-option "command-line"))

```

EDIT: I edited my answer to check for both Mac (system-type) and not command-line (window-system).