We have been using plastic storage cases that was designed for screws/nails to hold our Thomas minis. But we just picked up this spiffy new blue storage case from Walmart ($13) that holds over 50 mini trains!
The storage box is plastic and has a picture of Thomas in the front. It has side snaps similar to the other two collector's cases that are already out. The top tray removes completely to another layer for storage. An inset in the back of the case serves as a handle.
While the overall construction of the case feels sturdy, the plastic that connects the case together where it opens up may be a problem. Over time, I believe the plastic piece it will actually separate. The same is true for the two snaps on the side that keeps the case shut. For now though, this is a great way to store all those minis!