I sew both knits and wovens on my serger, and I change needles when I switch from one to the other (universals for wovens, ballpoint for knits). I don't discard my needles all that often; I do when it's obviously needed but sometimes I'll have only sewn a couple t-shirts and then be ready to switch over to wovens. I used to just keep the needles in one of those cases they come in, but I came up with something recently that I think is pretty clever. My serger tools (screwdriver for needles, big tweezers for threading, thingies to hold the thread in place when I'm not using cones) are in a little ziplock on my sewing table, and in that bag I keep a square of folded over knit fabric, and a square of folded over woven fabric. When I take my knit needles out of the machine, I put them in the square of knit fabric and then put that back in the bag. And when I'm set up to sew knits, I store the woven needles in the little woven scrap.
As an added bonus, when I take a break from sewing and can't remember what kind of needles are in the serger, now that I have this little trick I can just look at which scrap has needles in it and then I'll know which needles are in the serger.