This post is for you.
Now, the answer I've heard around the water cooler is "Stick it in the HEAD tag on your page, of course." Well if you're following best practice, your portlet has no business including a HEAD or BODY tag. Not only that, but by doing it that way you're asking for all sorts of interesting conflicts. There is a better way.
Your Liferay portlet includes, in your WEB-INF folder, a liferay-portlet.xml file, does it not?
It had better.
That's where you define your .js and .css class files for the portlet.
Inside the <portlet> element, you should have these two settings:
With those paths and filenames being relative to the portlet's own application directory.
Have more than one file to link? Use multiple tags and define each one individually.