Depends on the console & the box itself... if the box was designed as an easy-access holder to be used during the game's life, they aren't hard to find. If it was mostly a conveyance for sale, not so much.
For the most part, cartridge boxes are hard to come by, since they weren't very necessary & took up a lot of space. Intellivision used a gatefold style box for most of their releases, so those are pretty common. Genesis/Master system boxes too, since they mostly took the form of plastic keepcases. Although oddly, Master system manuals are rare. Not sure what's up with that. Pre-DS & PSP portable boxes are the hardest to get, given how much easier it is to just take a few carts places instead of a bunch of boxes.
CD boxes are much easier to get, since all of them double as protection for the discs. Obviously some disc-only games are out there after people moved their collections into CD wallets to save space, but it's not nearly as common as with carts.
You can get boxes for everything, but it's usually extremely expensive. For example: Legend of Zelda on NES, as a cart, goes for 20 bucks or less. The cheapest boxed copy on Ebay right now is $50. It is not at all uncommon for empty boxes to be worth more than the actual game, becuase they're so much harder to come by. While box art is pretty, most people don't display it- it just goes into a shelf with the spine sticking out. That's a pretty big investment of money and space for something you won't really look at- so, most collectors don't bother.