If you've seen the following message, it means that YouTube currently isn't enabled as a service for your Apps account:
YouTube is not available for domain.com. Learn more about Google products you can use with firstname.lastname@example.org. Did you use this product with a different Google Account? Sign out of your current Google Account and then sign in to the account you want.
How to add YouTube as a service
Only your domain administrator can enable YouTube on your domain. Let the domain administrator know you'd like them to turn on the ability to add YouTube as a service. Once they've enabled this, you should be able to add a YouTube account directly to your Google Apps account.
If you're the domain administrator, find out how to add services to your Google Apps domain.
YouTube can't be enabled for my domain
If you're in a country where YouTube has not yet officially launched, YouTube unfortunately cannot be enabled on your Google Apps domain. You can check which countries are launched in the Country dropdown at the bottom of any YouTube page.
You can still create a YouTube Account on a consumer Google Account separate from Google Apps.