[Plugawy]

Depends on what are you going to do - I created quite big apps in both jQuery and Prototype.

Whatever you want to do - you can do in both - it all depends on the size. I find Prototype better for big projects where you can use it's class system. It feels like Ruby as well.

jQuery on the other hand is small and gets the job done, but without a plan on how to structure your code things can get really messy.

[ionrock]

I felt this way before until they released their widget framework. It gives you a really good option for writing jQuery friendly javascript throughout your entire app. I don't know if that was the intent, but in terms of fitting an application within the scope of the jQuery framework, the widget features are great.

[Plugawy]

Oh, good to know - I haven't looked at jQuery since 1.2 since Prototype and MooTools where doing the job for me.