> AutoCAD/Blender and other 3D modeling tools also have good UIs once you go through the pain of mastering them
I'd like to add ZBrush and Houdini to this list. (Both of them are 3D modeling tools.)
ZBrush is known for having an extremely unintuitive UI, but once you figure it out it actually all makes perfect sense and generally you wouldn't want it any other way.
Houdini is weird because it's not very difficult for programmers to pick up, but it's very hard for everyone else. That's because it's literally a programming language for creating 3D models. As a Haskell fan I appreciate that the language is lazy, but aside from that it does leave something to be desired. That said, the HN crowd should be able to see why it's very powerful to create 3d models by programming them instead of by hand-manipulating a mesh (like you would in Blender or ZBrush).
Ableton (music creation software) is also extremely powerful but difficult to learn.
Lastly, it's not really a UI, but nix is a build system that's hard to learn but once you do learn it you can do things that would be very difficult in any other build system I know of.