Good question from one of our readers! HappyJeepGirl has some good ideas but I do want to take it one step further.
This has been a topic on my mind since we have started discussing the bomb shelter. My suggestion is to use a system where it recycles the urine back into the water drinking supply; thus, not running out. NASA is currently working the kinks out of their new system (ew, who would want kinks in their water supply?) but if it's good enough for NASA...
The other "stuff" can actually be used as fertilizer for the most part. So we can save this "material" in a special place in the shelter or we can dig a whole to drop this "stuff" back into the ground...like an underground outhouse. Add a few solar panels and a working system and this will become future compost in no time. Kind of what they do in some national parks with outhouses. At least in Kansas they do. :)
This way, nothing goes to waste (pun not intended but funny)...and we are not creating more waste than we can deal with. One of the reasons we are in the current state we are in, in terms of global warming, trash, etc.