I would use php includes or just use templates (if possible) in your web authoring software. Javascript might give you problems
SEO wise and will add unnecessary bulk to the page.
For example to use a php include simply give your page a .php extension and put the code below in it.
Code:
<? include('my_header.html'); ?>
Actually SSI is a server side include, just looked it up (acronyms!)
so that's basically the php option if you're server has php. You shouldn't need to mess with a .htaccess to get it working but it depends on your setup I guess.