Shopify's definitely doing integration right. The API docs are a little rough, but they've done the important parts.

I've spent the past few weeks helping new Improvely users integrate our tracking platform with all their different shopping carts. With most of them, we had to walk people through editing templates/themes or other kludges. With Shopify, we just wrote an "app" to register scripts with the theme, some webhooks and a few API calls, and the end-user just needs to click an install button.

Best of all, all those hooks/scripts get unregistered automatically when the app is uninstalled. Even other platforms that have a plugin/app system like this tend to get that part wrong.