Honestly, I find the manuals are a bigger deal than boxes. The boxes are nice for nostalgia purposes, the feeling of "oh yeah I remember when games came packaged like this," but oftentimes the manual is almost necessary if you don't want to figure out a game just by mucking around. Especially with like strategy games and the like, where not everything is self-explanatory.
So I'd rather have manuals.
For CDs and DVDs I absolutely will NOT buy non-CIB copies, unless they come really cheap. I only have two games that are missing manuals (Strider 2 and Xenogears) and both of those were basically given to me. Incidentally, if someone has some loose manuals...