<p>I can get simple examples to work fine as long as there's no master page involved. All I want to do is click a button and have it say "hello world" with the javascript in a .js file, using a master page. Any help very much appreciated :)</p>

Just move the
```
<script type="text/javascript" src="jquery.js" />
```
tag into the head tag in the master page. Then you can use jquery in all content pages.
There is no magic about using master pages with jQuery.