I do use DSU's for the stuff I want to accumulate large quantities like cobblestones, wood blocks, blaze rods etc but I was building up a huge amount of brains, lungs, muscles, sugar etc from my witchs (which also yield glowstone and redstone which I do want to keep) so I came up with a neat solution. I have a chest with a responder chip set to high priority filtering the stuff I want to dispose of but no broadcaster chip, then I have 2 more outputs on that chest, 1 that goes to another chest on the main network (with no responder chip on the network side, and a stock control chip on my trash chest side telling that chest what I want to keep) Then the last output on the trash chest has a partially upgraded extractor chip (stack size, not timing) and this goes into a nullifier. This way I have the quantities that I decide of certain items, and the rest gets trashed. The stuff stays in the trash chest long enough that the stock control chip has time to grab what it needs but not long enough that it overflows the chest.
I did some experimenting with the responder and stock control chips, and you can use more than 1 of each (in the appropriate spots of course) so you could in theory store 127 (max number of items that a stock control chip can handle in each matrix slot) of 27 different items in 1 chest with the rest of those items getting trashed. I can post a simple schematic if anyone is interested. It took me a while to come up with this solution, but so far it is working really well.
Thanks heaps for the nullifier advice StratusNightstar