Christian Heilmann lays out seven rules to better unobtrusive JavaScript, including not making assumptions about JavaScript, the browser and the document. Work with structured markup. If you are traversing a document, maybe there's a solution that can take advantage of CSS's selector mechanism instead. Work with browsers and users. Better understanding of events, and playing nice with namespace, scope, and patterns. And of course, think about the next developer, so keep the code maintainable.
An index of JavaScript's core methods, ordered by method name. No DOM methods are listed, but Browser Object Model (BOM) is.