Anybody know? I'd really like to pull it out & use jquery, but if the core Varien js is using it...
Scriptaculous is an add-on to Prototype, which is the actual framework that Magento is using. In a sense it is to Prototype what JQueryUI is to JQuery. So I don't believe you'd be looking to replace both. It be a very large task and probably not worth the effort. I actually found it easier to learn prototype than to go through the large amount of inline JavaScript (BAD MAGENTO) and replace it with JQuery.
Anyway, to answer your question, it's used all over the place in Magento. I believe it's most noticeable in the admin since it has a somewhat sophisticated interface. Pretty much anywhere you see Zooming, Sliders, Drag and Drop, etc. you can blame Scriptaculous. Nearly everything else JS related will be prototype.