Aside from Windows itself, I'd offer SharePoint as the most wide-reaching product that the company produces. To deploy and work with a SharePoint installation crosses all boundaries between servers to end-user software.
This being the case, a brief examination of a few pieces of it can illustrate the walls between the various groups.
Firstly, there are around 6 distinct People Picker controls in use through the product. That's the dialog where you pick a user from AD or whatever authentication provider you're using to either give them rights or attach them to something. All do exactly the same thing, some look exactly the same, and some look different. But there are 6 of them.
Interface customization in SharePoint is a huge mess. You can create an application page and deploy it to the server. You can customize other page types with SharePoint Designer. You can use InfoPath to customize list forms. Now you can even take some random HTML you made in a text editor or dreamweaver and run a process to create a new layout from that as a template. I could keep going about the various customization vectors (if you can think of another manner, I've probably done that too). Even the pages making up the functionality that ships with the product don't follow any sort of reasonable pattern. Sometimes you're looking at an InfoPath form, and sometimes an HTML form, and sometimes you're kicked to an application page that looks distinct from other application pages doing the same thing for other services. Some functionality is in web parts, and some are in delegate controls.
Go to the administration settings for PowerPivot, and you get something that looks different than the settings for Excel Services. Then look at PerformancePoint. All are serving very similar functions, and providing very similar settings, but it's like learning Mandarin and then needing to also pick up Cantonese to set up the next thing that is ostensibly part of the same product.
They've taken some steps to unifying parts of the product in SharePoint 2013, but there is still a long way to go before it can be called cohesive. If they can break down some of these walls for Microsoft as a whole, then maybe it'll make SharePoint more solid as an offering.
Then again, if it wasn't a mess and made sense I'd be an order of magnitude less valuable as a SharePoint guy.