I recently learned Smalltalk (Pharo), and since it's image based it treats classes/functions as more of a collection than trees of files. Of course, there's still structure, but the way you can navigate from function to function is great.

Smalltalk of course has its own problems. It suffers from one of the major problems of many less popular languages, namely the lack of libraries. But I agree that I wish more (or all) languages were as good at debugging, peeking at definitions, jumping to different things, searching code, etc. Of course editors can make up some of the problems, but it's not quite the same.