In back office applications we can use whatever framework we want. It is used by a small number of people and we have total control over possible dependencies and namespace collisions, so we do not have to worry about breaking other people’s stuff.
When we create code that is going to be included on another web page it is a completely different story. In those cases our goal will be to create code that does not require a framework, so we avoid polluting the requiring site with our dependencies. It might not always be possible to achieve this, but it is a noble goal at least.
We also find that Prototype (and Scriptaculous) are lacking in regards to their option for “plugins”, like calendar- or graph-plugins. Either Scriptaculous have a solution built in, or there are very few good alternatives. Both JQuery and YUI seem to have better communities surrounding them that develop better, and more, plugins that might suit our needs.
Another option in regards to plugins that we are going to look into is ExtJS. The GUI elements that they offer seem to be very powerful, and using pre-built items would save us a lot of time. The pitfall that we saw was that overuse of the items they supply might make the application look too much like a desktop application. Since we are developing for the web we should be careful to not draw too much inspiration from the desktop, they are different media and require different solutions.