My application is very database intensive so I\'ve tried really hard to make sure the application and the MySQL database are working as efficiently as possible together.
You should be easy on increasing your cache, it is not only a "not that much available mem" thing!
Reading for instance the manual you get this quote:
Be cautious about sizing the query cache excessively large, which increases the overhead required to maintain the cache, possibly beyond the benefit of enabling it. Sizes in tens of megabytes are usually beneficial. Sizes in the hundreds of megabytes might not be.
There are various other sources you can check out!
A non-zero prune rate may be an indication that you should increase the size of your query cache. However, keep in mind that the overhead of maintaining the cache is likely to increase with its size, so do this in small increments and monitor the result. If you need to dramatically increase the size of the cache to eliminate prunes, there is a good chance that your workload is not a good match for the query cache.
So don't just put as much as you can in that query cache!
The best thing, would be to gradually increase the query cache and measure performance on your site. It's some sort of default in performance questions, but in cases like this 'testing' is one of the best things you can do.