I've always been a Prototype advocate. Not for any deep down reason for how it compares with jQuery though, mostly because I was interested in learning Ruby on Rails and it happened to be the library of choice. With version 1.0 of jQuery hitting the shelves over the weekend, it's a good time to re-evluate the reasoning behind this. Luckily there's great posts out there advocating both for prototype and Why jQuery's Philosophy is Better . Interesting food for thought. Look forward to reading over jQuery 1.0's source.
Prototype vs JQuery?
Published August 29, 2006 on adamfortuna