Several of my pages use both JQuery and Protoype. Since I upgraded to version 1.3 of JQuery this appears to be causing problems, because both libraries define a function nam
If I were you, I'd drop my no conflict code into a JavaScript include file like you opined about above, and then figure out some process where I'd be setting these things I need to include in all my pages in one central place. If you are working with straight HTML files and you don't have any kind of templating/scripting capability server-side for what gets included in a document, there's always the possibility of doing a Server-Side Include.
Either way, the pain you'll experience updating each of your pages this time will come back again when you need to update your analytics code or the site footer.