I've been using jQuery with Prototype (already having remove scriptaculous) for a while now at Zivity (slowly working our way to a Prototype-free world). We run jQuery in no conflicts mode: var $j = jQuery.noConflict(); with prototype loaded before jQuery in the head.
On the branch I'm currently working on I have jQuery 1.2.6 running in no conflict next to Prototype without any problems. Regards, Wil Everts [EMAIL PROTECTED]