What makes great web sites or apps great are not always what you can see and experience. Actually all the great apps i know have wonderful hidden features. Those are not features you need to search in order to enjoy them. They are just there, in front of you. But they are just not visible.
The most important and obvious features is speed. Remember when you first discovered Gmail coming from AOL mail or Yahoo mail. It "felt" fast. Messages were opening fast, sending was fast....
It was the best new feature ever brought to an webmail.
But most unvisible features are not visible because they have to do with how the developers have created the experience, so it feels natural to use it again and again.
Facebook's best invisible features, is in my mind, is how the page auto refreshes as you scroll. It does not feel that it is loading. It feels like it is there.
Google's best invisible feature is the way their spider indexes and structures new data so it becomes searchable.
From a user perspective: all is obvious, natural. You don't even feel there is special there. But it is there. and it is not easy to make it work well.
But you should not create an invisible feature because it's cool or you can brag about it. It should only serve one purpose: make the experience much better