I believe the item list sections off stuff (items, weapons, armor are in their own areas), but it couldn't hurt to try I guess.
I don't think you can make items that are not weapons to "throw" w/o doing some ASM hacking. You could do either one of the following...
1) Hack the item command to be usable for particular characters, so that they can use specific items like Paladin Cecil and the Crystal.
2) Hack the throw command to be able to "throw" special items that execute a magic effect. This may be tricky, but remember that "throwing" weapons that are equipped has the same effect as using the item-weapon behavior (it shares the item command after all). Perhaps this may give you some ideas to work with.