Managed Metadata is definitely a contender, but I prefer to favorite features of the Foundation version. I don’t know, I just don’t consider MOSS or SP Server as ‘SharePoint’ but rather first-party addons to SharePoint.
As such, my most favorite feature has to be the new service application framework.
Despite what some people will have you believe, Service Apps aren’t hard to write or even scary. It’s a bit like custom field types; if you don’t know what you’re doing, it’s like brain surgery with boxing gloves and a hatchet. After you get the flow of it, it’s beautiful.