A few great Javascript Libraries and other Links that I used and which I'd like to share:
1. Animator
Create perfectly smooth animations with this library, you can even use CSS to describe the animation transitions. There's probably no animation idea Animator couldn't handle.
Easy to implement and fairly easy to use.
2. Lytebox
A packed, single file version of the Lightbox 2, which is great for overlaying pictures on your website. Particularly great for galleries, as it let's you navigate through the images.
Very easy to implement and very easy to use (just add a rel parameter to your linked images)
If you want intuitive file management, then drag&drop in trees is the way to go. The gurus at dhtmlgoodies.com offer you one good implementation of that. Though it took quite some adjustments for me to get it working smoothly, it was a great help to me.
The one thing HTML4/XHTML is missing: Multiple file upload within one dialog. A great tool to make your uploads more user friendly. A bit hard to set up though.
I haven't used this one yet but I'm planning to implement this into my website. One problem with making a website fully AJAX is that the functionality of the history button gets lost. This lib is one way how to bring it back.
6. PNGfix
IE6 is not the newest browser, but still being used by a lot of people. And one big frustration about making a website IE6 compatible is that it's lacking alpha transparency. This small script automatically fixes all PNG-Images in your source code through a microsoft filter. All you gotta do is to load the script.
A collection for fully customizable Web2.0 loading animations.
A great Firefox plug in that gives you many tips on how to optimize your website speed
9. Silk Icons
1000 Free-to-use awesome-looking 16x16 Pixel icons. I use them everywhere
A collection of free sounds