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Which one would be faster – a local web app gui made with something like qooxdoo or a desktop app? How much speed difference would there be expected? I would prefer creating a web app which could in the future be shared than creating a desktop gui which is specialized on certain gui toolkits.
There are so many variables that your question about speed would be impossible to answer definitively.
On the one hand, a desktop application has local access to all of its resources, and fast network access to a shared database. The computational load is spread out among all of the workstations. So theoretically, desktop applications are faster.
On the other hand, in a web app, you are not transferring large amounts of data to the workstation, but only display markup. As the computational resources are mostly concentrated in one place, management and maintenance of the software becomes much easier, as there is no software installation required on the workstations.
In addition, Javascript allows some intelligent work to occur on the browser, making it look more like a desktop application.
So there are far more factors to consider than just raw performance.