We have a medium sized .js file that we include in our web framework that I am porting over to SharePoint. However, I'm not sure how to go about this or what the best practice is. This is for a framework solution that will be used by other client projects, so it's best for it to be self contained and deploy-able, rather than requiring manually deploying files to the webserver.
Embeded resource is the best way and you don't need to use the ScriptManager to render it out (as AJAX is not configured OoB on SharePoint), you can just render it as any other client script resource (through the ClientScriptManager).
Best idea is the have an if ContainsScriptManager else UsClientScriptManager style. That way you get the best of both worlds