we have a big ExtJS (still ExtJs 2) application, which provides windows explorer like functionality on a Java EE server. We now evaluate implementing a new functionality; we could base this functionality on a jQuery plug in.
Is it recommended to use jQuery and ExtJs in one application? Or will I have to deal with side effects occurring?
You will not have to deal with any side effect. The only problems I ever ran into when I did this is if I tried to operate on elements that Extjs relied on being left alone. Just make sure that when you start operating using jQuery that you're working inside a div that extjs doesn't plan to mess with. The best way to do this is to inherit from Ext.Component and then operate inside the div it provides. Ext doesn't do anything inside this div so you should be ok. You can also tap into the resize functionality if you need to, though this is not really necessary.