I've started playing around with Chocolately and am suitably impressed. Is there an easy way of gathering all of the originally installed software and letting the Choco package manager know about them? I know I can script it in PS1, but if that's already there I'd be so happy.
In the current version of Chocolatey there is no built in way of doing this, no.
As you will see in the Kickstarter here:
https://www.kickstarter.com/projects/ferventcoder/chocolatey-the-alternative-windows-store-like-yum
One of the scheduled features of Chocolatey is the ability to "Synchronize with existing and remove programs", which is what I think you are after.