You can use "junk" weapons to craft special boss weapons using the soul items obtained for defeating them. Boss weapons need an upgraded weapon of a specific type -- greatsword, ultra greatsword, whip, etc -- as well as the boss's soul involved in the recipe. Keeping a weapon of each type is a pretty good idea if you don't know any of the boss weapons' attributes, in case you find that you want to make a particular one. You'll be able to craft these special weapons once you talk to specific NPCs.
EDIT: Nevermind, in DkS2 you only need the boss soul to make the item in question. I was thinking of DkS1.