During a conversion with John Resig at the FOWA he mentioned it would be useful to have a tutorial that explained what jQuery doesn't do that Prototype does and visa versa, and in particular how X process is done in each library.
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Below you can find the presentation I put together that goes through the core of both libraries and gives you a process by process comparison, explaining how to achieve each function in each library.
Prototype & jQuery
You can also download the Prototype & jQuery slides (mirror)
The slides should pretty much talk for themselves, but I welcome any feedback or questions you may have.