When I was at college studying Electronics and Computer Engineering, we used a piece of software called Proteus. This software took a long time to get used to due to its interesting key bindings and mouse usage.
To select a track in Ares (PCB Layout package) you Right Click on it. Hmm not too standard, but okay, I can live with that. Now what happens if you were to right click on that track again? That's right it deletes it. Here is roughly my thought train while using it (just having deleted a track by accident):
Uh oh, I didn't mean to do that. Ctrl+Z...nothing, Ctrl+Z...Ctrl+Z Ctrl+Z Ctrl+Z. Still nothing...Oh yeah, undo is U in this program...
It also broke convention on Saving (S), Loading (L), and Printing (P) amongst others. Admittedly these are kind of logical, but then again I could never remember whether R you Reload or Redo (I still can't remember).
Whenever I needed to make a PCB at university, we used software called OrCad. This software is immensely powerful, and can do more things in simulation that I can possibly think of. However it uses standard key bindings. And even after several years of not using Proteus, you know what? I still tried to double right click to delete things, S to save et all.
When I needed to make a PCB and the lab was unavailable, I download the latest demo of Proteus, installed it on my laptop and fired it up. Straight away I notice it's slightly different. Right click is still select, however a second right click now brings a context menu up. And a third right click deletes. Hmm. Ok I can cope with triple right clicking to delete. But the real change was the keyboard bindings, which had changed to standard windows style. Ctrl+S saved. Ctrl+O opened. It was amazing. It did however take me ages to de train my old habits. Sometimes I still hit U to undo.
The real revelation was that a company decided to change something that was obviously a specific decision, and make their product conform more to what is expected. This software was a bit of a pain to use, but simple once you got past the keyboard bindings. Now it is standard the difficulty users may have experienced has gone, making it a much better product overall.
Well done Labcenter! Now if only other vendors could be so thoughtful.