where to assign the materials?

In a scene with lots of objects, is it better to give each object it's material in it's own file or in the final file where i assemble them all together?
The problem is that  there are not enough slots (even with sub-material) but if I assign the material  outside the final file, it is hard to modify it later.
What is the best way to work?
Thank you.
Keren  

Think of the material editor as "temporary storage."  You can always select a material from the scene later to work with if you want to make changes--as long as you use a good naming scheme for your objects and materials, it shouldn't be that hard to edit later.  ;)