One can enumerate hundreds of difference between software from open source community and companies like Microsoft. There are fundamental things that cause the difference - the paradigm of programming, the architecture of software family, and development productivity, etc.
On the server side development platform for example, popular open source tools are the well known LAMP. Four pieces are done by totally different groups of people, on different time schedule, and with different design style. They are all good products without doubt. They work together very well for sure too. Coding something on LAMP feels super geeky, because you control everything from top to the bottom. Commercial software makers like Microsoft have some different considerations. For good manageability, installation, configuration, migration, and so on mostly have easy to use (at least try to) GUI. For productivity, many of the routines are abstracted and hidden away from the application developers. For example, in ASP.NET, post backs, event handler registration, page templating and all those kind of wiring work is hidden. Writing server side code feels more straight forward like writing desktop application. ASP.NET really evolves from a programming language up to a server side framework. With the Visual Studio .NET's help like IntelliSense, debug tracing on both server and client side, visualized server control customization with sample data, and so on, developers are more free to focus on the business logic of the software, which is critical for business.
Talking about the hot AJAX. Interestingly this technology was started by Microsoft when building the outlook web access. Because it is majorly for business rather than the consumers on the Internet, it didn't surface that much until Google Suggest and Maps made the splash with it. To code in AJAX there are a lot of plumbing work underneath to wire up the connections between the client side scripts and the server side handler, AJAX for ASP.NET wraps all these up and provide a few straight forward abstract controls to improve the productivity of the application developers.
There are debates in many companies and organizations about Wiki and SharePoint too. Again like the comparison between PHP and ASP.NET, SharePoint is more of a platform that contains Wiki features and many other capabilities. Wiki starts out to do collaborative web content editing, while SharePoint is designed to be the collaboration platform which integrates with Office suites, workflow, enterprise search engine, content management, SharePoint Designer (visual design tool), etc.
Open source software products are simple, developer-enjoyable, and inexpensive upfront. Commercial products are more business friendly, enterprise infrastructure oriented, productiviey oriented (sometimes productivity and developer-enjoyable are not well aligned :) ), and more expensive upfront. They have much difference in the fundamental design paradigm. Comparing the two different types of products really depends on the specific requirements rather than a religious belief.