I've been thinking exactly the same thing! My workaround so far has been to use IDEs that have some project management features, and separate the code into separate files.
Nice! I've started using files to separate logic, I recently went from 3 tiered (GUI/code/libraries) to 4 tiered (GUI design/GUI action code/data structures and algorithms/libraries) and added folders for elements (like a custom made back arrow image) and IO samples to run my programs on. Making my software structured like this has helped, but it's far from where you can see even a simple algorithm in it's graphical form that I see in my mind, as that algorithm would all be in a single section of my structure. I'll have to look into the separate files idea, though perhaps I'll build my own custom code editor, I'm skilled in things like that, perhaps I could pull it off.
For example, SAS Enterprise Guide lets you create a project flow like this: http://blogs.sas.com/sasdummy/uploads/egparallel4.png
Note some of the advantages: nice code structure, easy (minor) parallelization, easy code segmentation, ability to examine intermediate data, etc.
I haven't found anything nearly as useful for SQL or more general languages. I would love to see something similar in Clojure/Python.