See above.I am wondering which tens should one use in these kind of sentences. For example:
1. When we arrived to the station we noticed that the bus had been already waiting for us. No, "had been already" is completely wrong. You could say "When we arrived at the station, we realised that the bus had already been waiting for us for twenty minutes.
2. When we arrived at the station we noticed that the bus was already waiting for us. Yes (with the preposition "at").
3. I had been walking for hours when suddenly something hit me in the head. That's fine.
4. I had been walking through the desert without seeing any human beings. This is OK.
5.I was walking through the desert without seeing any human beings. This is OK too.
You could use #4 and #5 depending on which tense you are writing in. I think "any human beings" sounds a little unnatural. I would say "without seeing anyone" or "without seeing a single person". If you are going to use "any" then follow it with "human beings".
6. I was always feeling terrible whenever I had to travel abroad. No. This doesn't work.
7. I had always felt terrible whenever I had to travel abroad. Yes, if the past perfect is suitable for the context.
"I always felt terrible whenever I had to travel abroad" is more likely.