If you only care about performance, most of advice in this thread is flat out wrong, and is becoming more and more wrong in the SPA era, where we can assume that the page is useless without the JS code. I've spent countless hours optimizing SPA page load times, and verifying these results with different browsers. Across the board the performance increase by re-orchestrating your html, can be quite dramatic.
To get the best performance, you have to think of pages as two-stage rockets. These two stages roughly correspond to
<body> phases, but think of them instead as
<script>/*...inlined jquery, angular, your code*/</script>
<style>/* ditto css */</style>
<!-- inline all your templates, if applicable -->
<script type='template-mime' id='1'></script>
<script type='template-mime' id='2'></script>
<script type='template-mime' id='3'></script>
Since it costs you next to nothing to send this portion down the wire, you can expect that the client will start receiving this somewhere around 5ms + latency after connecting to your server. Assuming the server is reasonably close this latency could be between 20ms to 60ms. Browsers will start processing this section as soon as they get it, and the processing time will normally dominate transfer time by factor 20 or more, which is now your amortized window for server-side processing of the
It takes about 50ms for the browser (chrome, rest maybe 20% slower) to process inline jquery + signalr + angular + ng animate + ng touch + ng routes + lodash. That's pretty amazing in and of itself. Most web apps have less code than all those popular libraries put together, but let's say you have just as much, so we would win latency+100ms of processing on the client (this latency win comes from the second transfer chunk). By the time the second chunk arrives, we've processed all js code and templates and we can start executing dom transforms.
You may object that this method is orthogonal to the inlining concept, but it isn't. If you, instead of inlining, link to cdns or your own servers the browser would have to open another connection(s) and delay execution. Since this execution is basically free (as the server side is talking to the database) it must be clear that all of these jumps would cost more than doing no jumps at all. If there were a browser quirk that said external js executes faster we could measure which factor dominates. My measurements indicate that extra requests kill performance at this stage.
I work a lot with optimization of SPA apps. It's common for people to think that data volume is a big deal, while in truth latency, and execution often dominate. The minified libraries I listed add up to 300kb of data, and that's just 68 kb gzipped, or 200ms download on a 2mbit 3g/4g phone, which is exactly the latency it would take on the same phone to check IF it had the same data in its cache already, even if it was proxy cached, because the mobile latency tax (phone-to-tower-latency) still applies. Meanwhile, desktop connections that have lower first-hop latency typically have higher bandwidth anyway.
In short, right now (2014), it's best to inline all scripts, styles and templates.
EDIT (MAY 2016)
As JS applications continue to grow, and some of my payloads now stack up to 3+ megabytes of minified code, it's becoming obvious that at the very least common libraries should no longer be inlined.