Yes, I have used script.aculo.us. I have a love hate relationship with it. I was able to do some really cool stuff with drag and drop and animated divs, and what not, but when I really really started pushing it, it started to fall down.
Here was the scenario, I was building an ad-hoc reporting system where the user could select their tables and drag fields between the tables to establish the "join" conditions (kinda like access or navicat if you have played with their query builder). Then the user could drag fields from an available list and establish group bys and order bys. Well, I could do the drag and drop an it would populate nice little divs, but then if the list started to scroll, that is where things got really screwy.
What I found was there are a number of memory leaks in their program. Esp. where they attach a dom element to a JS prototype. If you dont clean these up properly, JS keep them around forever. You essentially have to "detach" the dom before you "unset" the JS object. Most people dont do that and bam, memory leak. Crockford talks about it in his video.
So I moved on to another framework, I have been using dojo. While it does not have all the wizbang stuff, it works and works well. It too is based on prototype so you get all the syntactical goodness of prototype with that library as well.
If you want to pay for a library, blueshoes is really nice and powerfull and really well tested. It has been around the longest, so it has most of the kinks worked out.
Hope this helps, good luck in your endeavours,
Mike