To be fair, they got lucky a good many times. They wrote a BASIC interpreter (MITS even paid them to work on that) for the nascent personal computer industry that was mostly there when needed.
Microsoft's BASIC was the first language many of us learned to program in. The other day I solved Google's "are you a programmer" tests using both an Apple //e and a TRS-80 Model III (emulated with MESS). It was nostalgic.
I remember shopping for a new desktop PC right after OS/2 2.0 was launched. IBM charged more for a PC with their own OS (even though it included Windows) than for one with Windows alone, the sheer boneheadedness of that baffled me so completely the person on the other side of the phone taking my order thought I hung up. In the end, I forked out the extra US$ 50 or so and got the OS/2 box. The OS was really nice, very advanced for the time.
At that time, running a Unix GUI on a PC was a ludicrous proposition.
Seriously though, some of the biggest operating systems (my research area, OS virtualization in specific) advances have come out of Microsoft Research and Windows kernel development.
Care to list them?
http://portal.acm.org/citation.cfm?id=502034.502053&coll...
http://portal.acm.org/citation.cfm?id=233269.233330&coll...
http://portal.acm.org/citation.cfm?id=945445.945474&coll...
http://research.microsoft.com/en-us/projects/dryad/ is fucking cool if you're familiar with MapReduce.
There are a handful of IPDPS papers I also know of but can't grab because I'm off campus and my VPN to Northwestern is acting wonky.
Microsoft got lucky, once, by being in the right place at the right time (And having the right connections).
I'm not saying I agree with the OP or not, but any microsoft bashing that goes on is more than warranted. They have crushed businesses, held back innovation, wasted millions of hours of peoples lives trying to make IE not completely suck, etc
They do not innovate to improve users experience, they act to defend their monopoly. Look at the mozilla vs IE story. Once IE was dominant, they shelved development of it for years - it had served its purpose, which was to crush mozilla and hold back innovation of the web as a platform.