Thus far I have used them to make uncraftable items craftable (TiC Green Heart Cannister, DimDoors WorldThread),
improve mod-interaction (GC Oil -> BC Fuel, Alumite Pickaxe Head (Iguana TT) -> Terrain Smasher, MFR Laser Drill - TC4 Infused Stone, ),
hide items from NEI (CustomNPC's guns),
make crafting recipes harder (Draconic Evolution),
modify the ore dictionary (Pixelmon aluminium recipes, Extra Utilities Full Chest, GC Silicon, Choosing only one of each ingot, block or nugget type to be the output of recipes) and
create reverse crafting recipes (TiC Empty Canister -> Molten Aluminium).