What is the recommended way to include javascript files with web parts? For example, if I were to build a web part for a fancy box image gallery, I would need to include the plugin script (either via CDN or hosted locally within the site) as well as the initialization script on page load.

These are the three options I know of right now, but I don't like any of them and am hoping there is a better way:

1) I could put the <script> tags in the .ascx file, but that would load the scripts in the middle of the page which isn't recommended.
2) I could do something like a RegisterClientScript in the .ascx.cs, but pulling in client-side code through server-side code always feels wrong to me.
3) I could add a javascript web part to a template when I add this new web part. This is able to locate the scripts at the end of the page like I want, but it creates a dependency between web parts that isn't ideal.

What I'm really hoping for is something similar to how CSS styles can be included with a web part. Or if there was some system property of the web part that I could set that would always include my script files. How is this normally done?