I've just uploaded the HeroMachine 3 Alpha "Violodion Edition", which has a new button right next to the "Save as JPG" one that lets you "Save as PNG", allowing you to save your creation as a transparent-background PNG format instead of the lossier JPG.
Holler if you have problems with it. It should let you produce images that are slightly larger in terms of file size, but without the pixelation and degradation of the JPG format. Since some operating systems and browsers don't play well with
JPGs PNGs I am leaving both formats in. More options are more better!