Mootools! Definitely mootools - it's like stripped down, modified, cleaned and polished prototype. With a bit of work it can integrate with Rails nicely (using a Minus-mor), and the best part is that it encourages you to remove all the bloat from your own javascript classes, resulting in a lot cleaner code. I haven't used JQuery, but I'm hearing a lot of good things about it too, either way, prototype+scriptaculaus is just too fat for me right now (I've had pages where a "Document Size" query yielded a result of 105 K - 100K javascript + 4K html + 1K images ... that's just too much)
