For in-house development, I think it's more up to the company and the development guidelines. Some companies have standardized on web apps. But with click-once deployment and publishing of Windows apps so easy now, you can manage your versioning of Windows apps as well as web apps.
I don't do a lot of application development anymore in my current job (I do mostly database development now). But when the need arises, I develop Windows apps because I'm more familiar with them and because I can provide rich GUI functionality with ease. But really, there's probably one thousand pros and cons on each side. Off the top of my head:
Web Apps
--------
Pro -- by default, graceful crashes
Pro -- nothing to install (usually)
Pro -- easy to pre-load with application values (QueryString)
Pro -- more modular (think of adding pages to a site or portal instead of a self-contained .exe)
Con -- you need a web server
Con -- harder to provide rich client GUI functionality
Con -- sometimes web apps are less responsive (postbacks)
Con -- some functionality could be dependent upon the user's browser settings.
Con -- design considerations for different browsers.
Windows Apps
--------
Pro -- Easier to provide rich client GUI functionality
Pro -- More responsive
Pro -- Offload some processing to the client PC
Pro -- Rich custom controls
Con -- You may have to pay more attention to system requirements
Con -- Harder to integrate with other apps
Con -- Generally more debugging/potential for crashing (debatable)