I'm always hesitant to crash a thread like this by plugging myself, but as I've mentioned a few times - I do make and sell reproductions of game boxes. By that, I mean actual cardboard boxes with trays in them, not the plastic shells.... and not to toot my own horn, but they are very high quality as I've put tons of work into them over the years. If you wanna know more, PM me. Of course, they are labeled as reproductions. I don't do manuals because lord..... to actually do them the right way, would take loads of R&D that I'm just not willing to put in. Re-engineering a manual by hand? Such a headache.
If you want to go totally authentic, I don't blame you. Ironically, I'm the same way. In that case, I'd say stick to the boxes of your best games only. Or your favorites. I wouldn't bother with the cruddy games, but personally I don't even buy or own games that I don't like. Inevitably, you'll probably take a liking to a game that is missing one hell of an expensive piece of cardboard that you don't have. Which is precisely why I got into the box reproduction thing. It's cardboard. We were all stupid back then, and now people are taking advantage to the max. I've admittedly bought a $100 piece of cardboard before. Not proud of it, but sometimes you really want that authentic article. Carts just don't present well on their own. I don't like end labels personally.
Manuals, I think I can live without if I've got the box, but manuals don't run quite as much often times.
I've considered going 100% CIB for my N64 games, but there are a few that are just ridiculously expensive. A Bomberman Second Attack box? Yikes. So the only collection I'm going total CIB on is my Jag collection, because there's only a couple of expensive CIB ones and not many games all together that I want to get. As for my other collections I'll stick to just my favorites CIB, and then my own reproduction boxes for all the rest. Don't forget box protectors too, that's pretty much essential if you're going to buy a bunch of cardboard.