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Ghada Al-Sewwi , Quality Team Lead , Souq.com - a subsidiary of Amazon
Well I guess that one difference is in the cross browsers/ OS testing. In Web applications you perform checks on many browsers where this is unnecessary on desktop applications -since they are installed on your machine-.
Desktop software usually requires installation. Web applications usually do not.
But web applications are sometimes expected to be running 24x7. This can make upgrades and maintenance more of a challenge to plan and execute (and thus test)
In addition to browser versions mentioned by others here, you may need to worry about browser add-ons
You may also need to worry about the myriad browser settings that could cause issues with your web application
Some desktop applications are designed for single users. By definition, almost all web applications are multiple-user systems. You need to worry about concurrency, what happens when the same user is logged in multiple times, etc, etc.
Websites are Applications which are hosted on the Internet and intranet which are accessed using Browsers like IE, Chrome. It can be anything from ecommerce site to Time management or staff management, shift management built on technology which is hosted on Web platform
Desktop applications are installed on your Desktop, at times if its ERP you might need license to install it, as its cost is calculated per user. Here you need to have the software installed locally and then you test the application.
In addition to everything the guys mentioned earlier related to cross browsers & cross platform & the host of the aplication .. etc
There is the Methodology used :
In websites -> Mostly it's agile development
In Desktop application -> No specific methodology