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For all that it has fallen out of favour - even with the original author - I still find the OO-centric nature of Prototype much tidier and more elegant than the equivalent jQuery. For a language where objects are so central, it feels like the natural way to work.
jQuery has become so widely popular that it is not a framework that can be ignored, and it is great to see the huge array of community supplied widgets that operate as plugins. I just get a slightly hollow feeling inside when developing against it...