RetroBlit 2.1 ( • RetroBlit - A Retro Ga... ) features sprite packing support.
This video shows a visualization of the sprite packing algorithm packing 1000 png sprites into a single sprite texture. In realtime these sprites are packed in about 0.2s.
The left side shows the sprites packed so far. The right side is an internal view of the algorithm tracking empty spaces (green), and filled spaces (red).