OpenRaster with JPEG and SVG
OpenRaster is a file format for layered images, essentially each layer is a PNG file, there is some XML glue and it is all contained in a Zip file.
In addition to PNG some programs allow layers in other formats. MyPaint is able to import JPG and SVG layers. Drawpile has also added SVG import.
After a small change to the OpenRaster plugin for The GNU Image Manipulation Program, it will also allow non-PNG layers. The code had to be changed in any case, it needed to at least give a warning that non-PNG layers were not being loaded, instead of quietly dropping them. Allowing other layer types was more useful and easier too.
(This change only means that other file types with be imported, they will not be passed through and will be stored as PNG when the file is exported.)