For emacs lovers, there is Org Mode, that could come close (permits to run code snippets).

But the UNIX-style ubiquitous notebook is sh(1) :)

It is about taking the approach of having various helper programs communicating by simple common formats (with glue to adapt between them), scripting them in whatever lang you want...

The biggest itch for me is keeping a clean history. I could appreciate a shell that make a good distinction between the program output/input and the rest: I could benefit by having each output piped onto some pager/buffer so that I can select a past buffer and copy the raw content for instance...

This permits to run the command, and then only consider that you want to do something else with the output, like piping it even though it is already out...

That thing might pretty much be called emacs (yet a different approach), but emacs is way too harsh to me.

Maybe you could give acme or UNIX-only derivatives a try, which blurs the border between buffers, shell, editing, running command input...