It's been quite some time since I wrote my original post on optimizing the query cache, which set out a plan for testing improvements. Unfortunately I can't recall the dates of all the changes I made, and the server workload hasn't been consistent, but I think some trends can still be recognized.
The big question I had initially was if whether changing the value of query_cache_min_res_unit could have a significant effect on the query cache's memory utilization, and correspondingly reduce a high prune rate. The default value of 4K was almost twice the average size of a stored result, so I planned to reduce the setting in 1K increments and observer any effects.