Zuckerberg's thesis is that eventually all software is going to be social by default. Does social just mean "it has my friend graph?" No. It means it has access to all of the things your friends are doing right now and ever. And it also means it has access to all physical and virtual entities connected to you. The music you've played, the photos you've viewed, the videos you've watched, tracking all these things are possible today. In the future it will mean every little thing you do is getting logged by a big server in the sky. The places you go, the conversations you have, the things you look at, touch, smell, and taste. Facebook's goal is to be that server that all that data streams into. This is the reason that Google is shitting their pants trying to "iPhone" them by creating stuff like Google Glass, since unless they leapfrog them Facebook will be a large part of the "world's information" they cannot organize. It has nothing to do with search not being "social" (another red herring), it has to do with Google being left behind as Zuck spends 10 years rewriting the rules of the game, much like how Microsoft is suffering due to Steve Jobs doing the same. It's one thing for Facebook to make Google search obsolete somehow, its quite another for Facebook to make all software Google writes, now and in the future obsolete, which they are poised to do.
As for Microsoft, their investment into Facebook might be looked back upon as the smartest business transaction of the 21st century, if it gives them special privileges in building systems that are enabled by the data Facebook can give them. 2000-2010 might just end up being a "lost decade" for Microsoft, and they may yet come out ahead in the future of software in a way Google will be unable to. (And Amazon, as an aside, will be selling AWS pickaxes to everyone the whole time.)
All apps of the future are going to either be connected to the pulse of this feed of information or they are not. The ones that are not will slowly but surely be replaced by those that are, since they will be not just inferior but essentially braindead.
We are still in the playground stages of all of this since Zuckerberg is still plugging together the pieces. The stuff being built now is just scratching the surface since we don't know what we're doing and there are still gaps in the availability of this data. There is also a generational gap. Most people on HN cringe when they have to accept a Facebook dialog. Our younger siblings and kids will have opt-ed in to the big server in the sky in full, no holds barred, when they turn 13. By 18 it will be a distant memory that these choices were even made, and that they were choices in the first place. And by then they will be fully profiled by data mining algorithms, using software that knows them as well as their parents do (if not better.) And, for most software, opting out will mean the software basically doesn't work.
Once we are there, Facebook is essentially going to be able to implement a tax, much like Microsoft did for many years. Its hard to imagine how they will be usurped if they manage to get to this point, as they will be more integrated into the fabric of our lives than any other business I can imagine. More than banking, more than the utility companies, more than any retailers wet dream. Even more than Google. They have a strong technical team and a young, visionary founder who has absolute control of the company.
What could go wrong? Eventually we might see an anti-trust suit (think 2016-2017 time frame) but Google is doing its best to create the illusion of competition on that front. And, of course, Facebook still has (and will always have) a bus factor of 1, which can't be very reassuring to investors. If you step back and look on a 5, 10, 15 year window, though, you'll realize they are essentially unstoppable.