The list that Dori posted is pretty comprehensive, and I don't think that its possible to list all the libraries out there since there might be one being written even as I type (it seems to be a passion for some people).
I feel that going with jQuery and/or prototype will probably get you off the ground and building neat stuff pretty quickly, and chances are that you will fall in love with them as so many of us have.
Gucci had Thomas Fuchs (the creator of Scriptaculous) create their website without using Flash, but check it out, it looks amazing for being JavaScript / CSS only:
http://www.gucci.com
Here's a post about it:
http://ajaxian.com/archives/gucci-relaunches-on-scriptaculous
These libraries are so powerful and versatile (with some nice plugins) that you won't "hit the wall" and start looking to other libraries anytime soon.
I have also seen people do some nice stuff with Dojo and extJS, but I have never worked with them myself.