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Sure. You can use anything you like. Personally, I like the MooTools and MooFx libraries. Just make the usual links to them in your template header, or use the regClientStartupScript() and regClientScript() functions to load them through a snippet on pages that use the javascript effects.
The only issues you might have is if you are logged in to the Manager and have QuickEdit enabled; since it automatically adds the Prototype and Scriptaculous libraries to your document’s header it may cause conflicts with your libraries. But you can easily enough disable the QuickEdit plugin if that’s the case.