Whenever I think of Past Perfect, the first situation I imagine is 'a skiing accident'.  In itself, it's a bit limited and you need to make it clear that 'skiing' is a gerund (otherwise they might mistake it for Past Perfect Continuous), but it can be quite good, and is easily extended to the following trip to the hospital, etc, to provide more examples.

Here is rough outline, based on that:

1. In 2005, Tom went skiing.
2. He had been skiing several times before that.  (eg. He went skiing in 1999 and 2002).
3. On the skiing trip in 2005 he broke his leg.
4. When he wanted to go home, he crossed the Beginner slope, slipped and broke his leg.
5. That was very unlucky, because earlier that day he had skied down the Intermediate 10 times without any problems.
6. He was lucky that his wife had gone on the skiing trip with him.  She was next to him when he had the accident, and she quickly took him to the hospital.
7. At the hospital the doctor put a cast on.  It hurt a lot. 
8. Tom was prepared though, because he already knew what it was like - he had broken his arm the year before.

This could be developed into a short story for them to read before doing the discovery tasks, or you could use pictures and timelines to present the situation and try to elicit the different examples from the students.

I'd like to hear other people's suggestions too, though... because this is the only one I think of every time I think about Present Perfect.  I'd like to experiment with a Murder Mystery context (for variety and interest) and something businessy for the Business English groups.  Any ideas?