I haven't tinkered with ZC in quite a while, so I don't know if it's been a feature already or not. Forgive me if I end up sounding like an idiot and this is something we've already got and I just didn't notice.
So, let's say that you're working on a really big and complicated quest, or you rip something that was really repetitive or complex, or you're the kind of person who rips everything that looks useful, but you end up not using a lot of it. You end up with a ton of tiles that are identical or only a pixel or two different from each other. It would be awesome if we had a way for ZC to scan the Tile Pages and compare them to the Combo Pages, and then automatically removing every single Tile that isn't being used for a Combo graphic. Additionally, it's easier to keep track of Tiles when ripping an image by essentially assembling the image in the Tile Page, but that results in a lot of wasted space. A compactor option that just moves all of the used Tiles to the first available empty spot to make it easier to see remaining usable space would be helpful as well.
How this feature would be implemented, I'd imagine would be something like...
The user has the ability to right-click on a Tile in the Tile Page, and there would be an additional option marked something like "Lock Tile" or "Protect Tile". This would be for Tiles that are being used for scripts and not necessarily Combos. In a menu somewhere would be "Strip Tile Pages". This would bring up a window that would ask for a setting. Either remove all duplicate Tiles, or check all tiles and remove ones that are only one or two pixels different from each other. Any Combos that are set to these duplicates would be automatically changed to instead point at the original that's saved, preventing most opportunities for things to break. (This setting window would probably include a warning to save a backup of the quest file anyways, just to be on the safe side!) As well as comparing Tiles against Combos, it would also check things like Enemies or Items to know other ways that Tiles are being used.
The "Compact Tiles" setting would essentially do just that. It would start at the very first space and check if it's empty. If it is, it looks ahead for the first non-empty, non-Protected Tile, and move it to that empty spot. Any references to the tile being moved would automatically be changed to the new location. It would then move to the next empty spot and repeat the process. In the end, the filled Tile Pages would probably be more difficult for the quest designer to parse through and make changes, but any and all empty space would be much easier to work in, and pack more into. Alternately, if you could selectively pick groups of Tiles that you want to apply the Compact setting to, you could work on an area like a Dungeon, and then when you're finished and no longer need to touch those Tiles anymore, pack them away when it's time to move on to the next section.
Like I said earlier, a feature like this would be incredibly useful for ripping graphics, making huge and complicated quests with a lot of differently-themed areas, or if you're just rather disorganized and would like to be able to just pack everything down from time to time to give yourself a bit more working space.