Cost.
Over the life of the software use, web applications are typically significantly more expensive over time. Desktop applications are purchased outright and rarely is their a recurring fee for the software use. Some desktop applications do have maintenance fees or fee based upgrades associated with them, but rarely is there a subscription fee associated with the software's ongoing use.
Many corporate web applications use a different model, users typically are charged monthly service fee to operate the software. Fees are considered "subscription fees". If you fail to renew your subscription you may be unable to access the data stored in the web application.
Connectivity.
Web applications rely on persistent and unmanaged connectivity. If you do not have an Internet connection or if your host does not have Internet connectivity you cannot access the information. Critical applications or businesses that are time sensitive cannot risk denial of service attacks or power outages to interrupt their operations and access data that is sensitive.
Slower.
Web applications that rely on the Internet to transfer data rather than a computer's local hard drive, may operate slower. The speed may also vary based on number of users accessing the application.
Backups & Ownership.
Regardless of the platform, companies need to be sure that their data is appropriately backed up. When using a web application that are hosted by a third party, companies should clearly determine who owns the data housed in the application, and be sure that privacy policies prevent that data from being used by the web host.
Ultimately the accessibility of web based applications make them very desirable. Web applications have some fundamental limitations in their functionality, and are better suited for specific tasks. Understanding the pro's and con's to each business model, will help users determine whether a desktop application or web application will better suit their needs.
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