Right now they can be an annoyance, but this is something that could easily become a great feature of github, the same way that @tweets and #hashtags innovations came from the twitter community.
I would love for github to make bots something that you can subscribe to on a "bot subscription page". I think they can be incredibly useful so long as they aren't promiscuous, unwelcome and frequent enough to be seen as spam. You should be able to handle these the same way you handle permissions for third-party apps on Facebook or Twitter. The subscription page could also provide bot ratings and suggest bots that are likely to be useful for your project.
This approach would also create a way where these apps could be useful for private repos as well.
I would love for github to make bots something that you can subscribe to on a "bot subscription page". I think they can be incredibly useful so long as they aren't promiscuous, unwelcome and frequent enough to be seen as spam. You should be able to handle these the same way you handle permissions for third-party apps on Facebook or Twitter. The subscription page could also provide bot ratings and suggest bots that are likely to be useful for your project.
This approach would also create a way where these apps could be useful for private repos as well.