Software I've created to fulfil specific requests that I think other people may find handy. This software is free unless specified otherwise.
As good as the Mac App Store is, app developers can’t offer demos or paid upgrades through the Mac App Store, and neither can they communicate directly with their customers if they have a problem. If an app is in the app store, developers have to pay a cut to Apple when you purchase it. Apps listed in the Mac App Store must run in a restricted 'sandbox' environment - they have only a tiny little container they have access to, and they can’t communicate with other applications.
(A good example of this is the Clam Antivirus scanning engine. The version downloaded direct from the Developer's website contains a realtime scanner - an icon that sits in your menubar next to the time and alerts you the second an infected file is found. The Mac App Store version doesn't have this ability.)
There are many other limitations like these but it’s not just about individual limitations. The 'app sandbox' is something that was added to Mac OS X years after it was originally created, and it's not suitable for every type of program you might run on your computer. It's especially not suitable for the kinds of powerful applications you need to run on a desktop operating system like Mac OS X. Simpler apps like Twitter and Evernote can fit on the Mac App Store just fine. But more powerful applications that need access to more of your Mac (Adobe Photoshop for example) have to be distributed from outside the app store.