While working on a Joomla! site lately, I had an interesting issue arise. None of my scripts or CSS styles would load on a Joomla site installed on a subdomain. Luckily I was able to solve this quickly.
As it turns out, I had RewriteEngine turned on for the main domain and no .htaccess set for the new site. I ended up solving my problem by renaming the htaccess.txt from the new Joomla! install to .htaccess, then editing that and setting RewriteEngine to "Off". Problem solved.