I have an old M1841 "Mississippi" Rifle, all original and in pretty good shape. There is a threaded hole in the wood within the recess of the patchbox, up near the hinge of the patchbox cover, that has an original spare nipple screwed into it. That was smart... A good place to keep a very small but necessary part, where it wouldn't get lost. It is my understanding that all of the original Mississippi rifles were outfitted with a spare nipple that way, and the "patchbox" was actually more of a "toolbox." The standard issue combination tool, which had a nipple wrench and two screwdriver blades, and a worm or "wiper," and possibly a ball puller, were all intended to be kept in the box. I would assume they would be stored in there with a hank of tow, which would keep the tools from rattling around and would also be used for wiping the rifle's bore.
Granville Stuart reported a neighbor of his, in Iowa in the 1840's, had a half-stocked flintlock rifle with a silver patchbox. It was used for keeping a couple of spare flints and a greased rag, which was used for wiping down the gun.
We have an old Tennessee rifle in the family that has an iron "banana" patchbox. It appears to have remnants of dried-out tallow in the corners of the recess.
I don't own a shootable rifle with a full-sized patchbox at this time. If I did, and the lid was good and secure, I would probably keep a worm, a couple of extra flints, a extra pick wire, maybe a jag and ball puller, and some tow or cleaning patches in it. Small items that are used for maintenance but might be hard to keep track of. This would reduce clutter in the shot pouch.
I do have a couple of percussion rifles that have the smaller receptacles that are more properly termed "cap boxes." These, in my opinion, are too small to be good for much and are pretty worthless for anything but decoration, in my humble opinion. I guess these would be a good place to keep a spare nipple, though, screwed in place as on the Mississippi rifle. I suppose one could also keep caps in them.
It seems to me that a full-sized patchbox requires a considerable investment of labor to install, so they must have been intended for some practical purpose. However, what actually goes into the "patchbox" was, and still is, up to the rifle's owner.
Best regards,
Notchy Bob