Ultimately, there's just one way to ensure you're getting the best price: research. Check the Mac App Store and the developer's Website; the Mac App Store's product pages usually has links to the developer's Website.

Beyond the financial benefit, Mac App Store apps have also been pre-screened by Apple. While there are certainly downsides to Apple's in the store, one key positive for consumers is the extra piece of mind that Apple's review process affords. You'll absolutely continue to encounter crashes and bugs in Mac App Store software, but you can buy with increased confidence that the app you're downloading isn't a total lemon--since Apple's reviewers have already signed off on it.

With Mac App Store purchases you don't have to worry about license codes (since your license for the software is handled by the store behind-the-scenes), or potentially sketchy payment processors (since all your purchases go directly through Apple).