I am assuming the worst possible situation here. I do firmly believe that OS X will eventually be just like iOS, and we are seeing a lot the industry adopt methods that Apple has pursued previously. My worry is that Microsoft, if they happen to release an App Store themselves, will go down the same path. They have done this with WP7 and the Marketplace.
It's a slippery slope releasing an App Store IMO because I don't want to own a Mac that will eventually be locked down like the iPhone, and since that method will "most likely" still be a success, other companies, including MS, might be curious to adopt this.
Is an App Store bad? Hell no.
Is the way they are being implemented in our every day technology bad? Hell yes. Even on Android phones with AT&T you can't install from unknown sources. Granted, Android phones in this respect are not the norm, and thankfully so.
In short, let's all proceed with caution.