I have thought about using HAM mode as part of a 3D engine, where the "hold" effect is used to fill the polygons without needing to use the blitter (except for the outlines). Essentially if you fill the whole screen with the value that holds, for instance, the blue value, you'd only need to draw the edges to get any red/green/yellow polygon instantly with the hardware.
I haven't thought about it too hard, but I reckon a super fast 3D engine in 4096 colours should be possible (not texture mapping, just plain faces).