Ah, I have two methods for clearing my box. It's basically a combination of the answers available so I had to choose "Other"
Whenever a new PM arrives to my box, I reply it. And after that, if the PM was not of much importance in my opinion, it gets deleted, because I know I always need some space for more people's PMs.
And, in case the PM was useful to me in some way, I leave it at the main folder (and sometimes, I send them to other folders I have created), once a certain time has passed, I run a checkout on all the folders to check the contents and if there're unuseful PMs, I delete them.
I always try to have a 50% of my PM box clear (which by now is starting to fill up), I dont like to see too much mess...