It gets very annoying when you pick up a bunch of unwanted items and it can clog your inventory fast. So, why not add an item filter to filter out certain items in player settings?
Next to what tower said; EMC is ment to be Vanilla+ I would see this as something for modded minecraft (I beleve Tekkit (minecraft full 1.0), the only modpack I played, had an item that does that...) This would go too far away from the vanilla game I think.
If you want, I can setup a few chests for you to dump any unwanted stuff in? But, yeah, you can either drop stuff on the ground, throw it in lava/cactus/fire, give it to me, or use /dispose or /trash.
That is only of you alredey have it in a chest though. The OP is refering to how stone and such can fill up your inventory when mining and such, as, indeed, sorting thhough items when they're in a water stream (or hopper stream, if it's short enough to not cause too much lagg) alredey is quite easily doable.