ArenaNet’s Gaile Gray dropped by the official forums to post a little clarification around the company’s stance of 3rd party apps or mods, and goes on to give a few words of advice if you choose to use/develop one. 

The best way for a player to assess whether a specific third-party program could have any impact on another player or a PvP opponent is to ask: 
• “Does this program allow someone to play faster, better, longer, or more accurately than someone who doesn’t use it?”
• “Does this program allow someone to ‘play’ when he/she is not at the computer?”
• “Does this program allow the user to gain undeserved rewards?”

If the answer to any of these questions is “yes”—or even “maybe”—then we strongly recommend that you do not use the program because to do so may place your Guild Wars or Guild Wars 2 account in jeopardy.

In addition to the providing a few guidelines, she also mentions one more thing: 

In the future, we will be working directly with the community to develop app support for Guild Wars 2, so stay tuned for more info!

Does this mean a possible API or toolset release to aid the development and mod community? I guess we’ll just have to wait and see.