This is worth a blog post since it turned out to be a task that took me 15 minutes to complete...
I wanted to sign up for Google Checkout as a seller and tried to sign in with my Google Apps account. The error message I got told me that my account was not enabled for Google Checkout and that the administrator for my Google Apps domain had to enable it.
Luckily that administrator is me so I went on the hunt for the option that enables Google Checkout for my Google Apps account... 15 minutes later I found it, and to save you some time here it is:
1) Go to your Google Apps account at https://www.google.com/a and log in as the domain admin. You may find it easiest to simply log into your Google Apps GMail account instead in which case you now need to click on 'Manage this domain' at the top right.
2) You're now on the Google Apps homepage for this domain. Click on 'Organization & users' (second option, top left)

3) Next click on 'Services' (next to the selected 'Users' tab (it's easy to miss).

4) Scroll down to 'Other Google Services' and past it until you find Google Checkout. Turn it on.

You are done!