Apple just released the Mac App Store, and with it came one very unfortunate feature. It was well-intentioned, but poorly executed, and it ends up being an "attractive nuisance," meaning that it's something that you're really better off ignoring: third-party apps not purchased via the Mac App Store may appear as "Installed" there, leading to unrealistic expectations of what you can do with Apple's latest service.
Here's a quick overview of how the Mac App Store works, in case you haven't tried it: 1) you search for an app, 2) when you find an app you want, you click on the button showing "Free" or "Buy" with the price listed, 3) the button changes to "Installing" while the the app is downloaded to your Applications folder and 4) the button changes to "Installed" when the app is fully installed.
The problem is that the Mac App Store also recognizes apps that you have purchased outside of the Mac App Store if the version of the app matches the Mac App Store version exactly, using something called the "Bundle ID." For example, if you noticed that the Mac App Store showed iPhoto as "Installed," even though you bought it through the boxed iLife set, but the Mac App Store did not notice that you already have Pages installed, it may be because you haven't installed the latest iWork update.
As you might expect, this has led to quite a bit of confusion, so it bears repeating: if you have not purchased an app through the Mac App Store, you cannot re-download it or get any future updates through the Mac App Store. For that, you will have to continue to check for updates using the app's built-in mechanisms, or check the developer's website. The folks at Panic and Barebones have written very good posts about this, as have the folks over at Macworld, so check them out if you're still unclear about how this works.
It's also worth pointing people to the "single serving site" of the day, called http://IfIBoughtYourAppAlreadyCanIUpdateItThroughTheMacAppStore.com, which seeks to answer the question that Mac developers across the globe have been hearing all day: "If I bought your app already, can I update it through the Mac App Store?" Spoiler alert: No. You can't. It's a different app with a different license.
That does not necessarily mean that you have to buy the app again. Many developers will continue to release apps both through their own websites and through the Mac App Store. I expect that what will happen is when the next major version of an app is released, most relatively inexpensive apps will move to be "Mac App Store-only" so that the developer doesn't have to manage two different versions of the app (one for Apple's store and one for their website). For example, Pixelmator version 2.0 will be exclusively available on the Mac App Store. Customers who choose to keep using version 1 can do so, but all future versions will be on the Mac App Store. The benefit to developers is not having to deal with billing and bandwidth charges. The drawbacks include no way to offer upgrade pricing to existing customers. Fortunately Pixelmator is now only US$30 instead of $60, so even existing customers can consider $30 a reasonable "upgrade" fee -- or continue to use version 1, which doesn't expire!
Omni Group's Ken Case mentioned on Twitter today that Omni Group will continue to sell its apps through its website for the foreseeable future, because it can "offer more flexible terms and options: upgrade pricing, bundle and volume discounts, and access to beta releases" and personal educational discounts. He has also written about it on Omni Group's company weblog.
The emergence of the Mac App Store is going to bring with it something like labor pains. Although I've never experienced labor, I've heard many women say that as time passes, the memory of the pain decreases. (Our son is eight years old, and I am just now getting the feeling back in my left hand from when my wife squeezed it during his delivery!) In a few years, many (if not most) apps will have moved to the Mac App Store, and new Mac customers will largely never have to deal with the problems that existing users are facing today. The fact of the matter is that if you want the Mac App Store version of an app, you have to buy it for the regular price, regardless of whether you've paid for every version of it up until now or whether you are a brand new customer. Upgrade pricing may be available through the developer's website, so be sure to check if you're not sure.
What do you do if you see that an app is listed as "Installed" but you're not sure if you purchased it through the Mac App Store or not? Simply click over on the "Purchases" tab at the top of the Mac App Store and see if the app is listed there. If it isn't, then you bought it somewhere else, and the Mac App Store is just identifying that it is installed.
One Final Tip
Several people have asked what to do if they want to download an app from the App Store but it already appears as "Installed," even though they didn't buy it from the Mac App Store. First, quit the Mac App Store, then remove the app from your Applications folder and put it in the Trash (don't empty it yet, just in case there's a problem and you want to recover it). Relaunch the Mac App Store, search for the app again, and it no longer appears as Installed.