This is a huge mistake for both companies, and would be tragic for pretty much everyone involved.
GitHub has become the open source hosting site for code, and for a number of companies, it also hosts private repositories. It's the place to be if you want your code to be found and used by other developers, and frankly, its so much of a de facto standard for this purpose that many tools and services work better with GitHub.
GitHub was founded on the back of Git, which was invented by Linus Torvalds to solve source code management woes for the Linux kernel. (Previously the kernel used an excellent tool called BitKeeper for this job, but some missteps by the owners of BitKeeper drove the Linux team away from it. It looks like GitHub is making similar, albeit different, commercial missteps.)
Microsoft already has their own product, Visual Studio Team Services, which competes with GitHub, but which frankly appeals mostly to Microsoft's own developer base. I don't think it is widely used by Linux developers for example.
Implications for Open Source
Microsoft has been much more "open source friendly" of late, but I have to admit I still don't trust them. I'm hardly alone in this.
It also is a breach of sorts of an unwritten trust that the open source community has placed in them. There is much bad blood between Microsoft and open source software. Many of the most treasured open source systems exist directly in conflict to proprietary systems. Think about software like Samba, and Wine and OpenOffice. These were created as alternatives to Microsoft. Being acquired by Microsoft means that these projects will feel compelled to abandon GitHub.
As this happens, many tools and services that offer services that are tailored to GitHub (automated code review, CI/CD, etc.) are going to be rushing to find a way to offer services for alternatives, as their client base runs screaming from GitHub. (Back in February of 2016 I tried to leave GitHub, because of philosophical differences of opinion with their leadership. I abandoned the effort after discovering that too many of the external support services I used for these open source projects were either GitHub only, or could only be converted away from GitHub with large amounts of additional effort and big negative impact for my users.)
This is a watershed moment for GitHub.
I predict in as little as 6 months nobody will be creating new open source projects on GitHub.
Unfortunately, it's probably already too late for GitHub. Unless they were to come out and immediately deny any acquisition attempts, and make some public announcements recognizing the trust they've been given, and asserting the importance of honoring it, nobody will trust them any more.
Implications for Commercial Use
This is also going to harm commercial customers, driving them away.
Microsoft has many commercial ventures which overlap with those of almost everyone doing anything in software. GitHub being acquired by Microsoft will in one fell swoop make GitHub a direct competitor with vast amounts of their own customer base. (Essentially, your either a Microsoft competitor, or a partner. And often both.)
It's time to reconsider the cost of hosting in the cloud. I've been expecting a move back to on-premises storage and hosting for some time now, but this will only accelerate that.
Implications for Microsoft
Microsoft will spend quite a lot of money to acquire GitHub. But instead of acquiring a goose that lays golden eggs, they are going to have one that needs to be fed and turns that into fecal material.
At the same time, while this may help bolster some of the technology in VSTS in the short term, the reality is that most of the best stuff isn't that hard to build, and most of what GitHub has can be done on any cloud based system with sufficient storage and compute. Most of their tech is not tied to Windows, almost certainly.
The VSTS team will no doubt be impacted, and there will be a lot of pain and suffering attempting to more tightly integrate VSTS with the new adopted child. I'm sure there are redundancies that will be eliminated, but I expect part of what is going to happen is a shift in focus from providing the best experience for Visual Studio developers and making things work well on Azure, to figuring out how to more tightly integrate GitHub's toolset into theirs. Can you imagine trying to reconcile the differences between VSTS and GitHub's issue tracking systems? Yikes!
The uncertainty will annoy customers, and I suspect will drive them away from the existing VSTS stack. Whey they leave, they probably won't be moving to GitHub.
Like the proverbial dog with the bone looking at his reflection in the water while on the bridge, instead of having one bone, Microsoft's greed will leave it with none (at least in this space.)
I'm sure that the founders and investors of GitHub will make a mint taking Microsoft's money. Normally I'd applaud anyone with plans to part Microsoft from some of it's funds. But this move is just plain bad business.
As I mentioned above, Microsoft has their own product, Visual Studio Team Services, which competes with GitHub. This alleged acquisition of GitHub seems to me to fly in the face of anti-trust rules. Microsoft clearly has been trying to make inroads into the open source community with projects like Visual Studio Code and Linux support for VSTS, so I would hope that the regulatory bodies involved would examine this with great scrutiny.
Of course, if GitHub is for sale, many of the same concerns except the antitrust legislation would apply. It would be a Bad Thing (tm) if GitHub were to be acquired by Facebook, Google, or Amazon, for example, for most of the same reasons that being acquired by Microsoft would be bad.
Now please pardon me while I go back to setting up gogs on my own systems...