It would be helpful if there was some way the cell library dialog could show recently used cells, at least from the currently attached library.
As an example, I am placing a lot of cells from a "Drainage" cell library. There are hunderds of cells here to sort through, but I am only placing perhaps half a dozen. Due to the nature of the work, it doesn't lend itself to "place all of cell A, then place all of cell B, etc." so i am switching back and forth between active cells fairly often. And each time, I need to scroll up and down through the long list of cells.
Cells that are placed in the DGN Model are already stored in the DGN header as definitions so it wouldn't be too hard to implement. You can see that when you enable Shared Cells in the Cell Library dialog and enable then display of Shared Cells. [Normal Cells are not displayed in this way through but can still be placed --> place Cell, detach library then place Cell again and it will be available.]
Or some sort of folder structure to organize the cells. This would go hand in hand with a folder structure to organize the models, as that's what a cell library is, a drawing full of separate models.
So to fix your problem, make a copy of your cell library, and delete the models spaces of the ones you aren't using. Made a mistake, there's an import models button to bring model spaces back across from the original cell library. The main trick is to realize a cell library is nothing more than a DGN with a different file extension. Then you realize you can just reference in the cell to save file size (this makes it a shared cell effectively). And many more tricks, more power to you :-)