Several applications released to the App Store, including Touch Dial Emoji [App Store] and Typing Genius [App Store], have included the ability to enable Emoji, but the functionality was included as part of larger applications with additional uses. Developers who attempted to release applications whose primary advertised function was to enable Emoji, such as Ars Technica's Freemoji, saw their applications rejected by Apple for their ability to modify settings outside of the applications' containers, a violation of the iPhone SDK.
Ars Technica recently interviewed Gary Fung, the developer of Typing Genius, who provided his perspective on the Emoji situation and how he has risked raising the ire of Apple by advertising his application's ability to enable Emoji, even going so far as to change the application's title to Typing Genius - Get Emoji.
Apple's acceptance of EmotiFun!, which apparently has made no effort to disguise its sole ability to enable Emoji, implies a loosening of restrictions on what changes an application is permitted to make to system settings, but whether this relaxation of policies will extend to iPhone features beyond Emoji remains to be seen.
Update: EmotiFun! has apparently been removed from the App Store, and it is unknown if and when it will return.