The best way is to keep them in a dry and clean environment. Dry cabinets , safes are good if the boxes r that valuable to u. I've a friend who packs his boxes in zip locks and then keeps them in his cabinet with a thirsty hippo , something u can consider as I can see his boxes end up quite well kept.
I've resorted to parking my IWC box in a dry cabinet to protect it. Those who own one will understand that IWC boxes are one of the worst around coming to durability. The sticky issue was enough for me to get back to IWC and they acknowledged the issue but prob won't do anything about it.
Comparingly , vintage boxes last superbly well - I've a 1950s Rolex box which is still in perfect condition despite being left in the wardrobe for storage generally. Ebel boxes survive remarkably well too.
Our environment is too humid to keep them and ... Frankly I'd spend more efforts towards keeping the watches well after all we paid mainly for the watch , not for box.
Yeap. Some brands do include a new box/pouch (of course not the original but still decent)when u send them in for general servicing. IWC, Ball all do.
As what Blur Shadow shared, using leather creams does go a long way to minimize cracking from overly dried leather. Keeping them ziplocks in controlled environments help a lot too. But really.. I really do attest to the drop in quality of watch boxes over the ages.
Since on this topic:
the most durable watch box I've :
from a quite young brand that some collectors are starting to take notice.
dropped it once on my parquet floor and (sob) , my parquet flooring dented ..
Just a modest collection, can't really buy as often as I want (pocket not that deep)
Personally I agree that it is silly to own too many watches but I can't help it especially if the design appeals to me.