I have two sub-folders for the initial intake of the list emails. I'm an attorney so one folder is for lists that are law-related. The other folder is for non-law-related stuff. Since this is read/review material it does not have any kind of commitment associated with it, as it does not pertain to me or my clients personally. This means that if I am doing some read/review, I can read from whichever folder I feel like at the moment.
I don't prune the inbox portion that often, as it is a relatively unimportant task. When I do prune it, I usually don't do it all in one sitting as that would just be too much time spent on something that is relatively unimportant. If it gets too big, I sometimes just wholesale delete all of it without even reading it.
I rarely prune the reference file. I really only do it when my Outlook starts running slowly. With Google desktop its always easy to find messages on a given topic or search term. The only reason to prune it would be if Outlook is starting to choke on its own data.
I regularly have the case where a set of messages becomes junk either because the law changed or because a more succinct thread came up months later on the same topic. When I need to refer to the information, if I find a thread that is out-of-date, not particularly useful, or duplicative of later threads I just delete it at that point. For instance, every month or two a thread may come up on the best software to help prepare estate planning documents. During read/review, most of these go to the reference folder. But if I am actually using the reference folder to search for that topic, many of those threads will be out-of-date or duplicative. It is when I am actually looking at the reference material on the subject that I trash anything that is a waste of space.
For me, the key to this part of my implementation is accepting that none of these emails actually matter to my life. They are there for only one reason. To make my life quicker and easier when I need information.
Think of the packrat who saves all old plastic containers. It is true that plastic containers can come in handy at times, but if you save every single one of them forever, your house fills up with them to the point that there is no room to move. Instead you just save a few that seem really useful and recycle/trash the rest. It's true that you may one day say, "that one I threw away would be really handy right now," but you just can't get attached to everything that might have some unspecified use in some unspecified future.
Email listservs are there for your information (FYI), which is not to be mistaken with actual importance, in my opinion.