Hi Rick
a few comments:

1. I can recommend that you try PovRay output. It is PNG, transparent 
background and much better look. You don't need to learn how to use 
PovRay, producing the images is straightforward. You have to install 
PovRay, export to PovRay format from Jmol and then save from PovRay to 
PNG

2. I do not think that JPG may have transparent bacground; it would be white 
maybe. And as Bob says, the quality is always worse -- the only advantage is 
smaller files, at the cost of quality loss.

3. Given the way Jmol works for rendering I believe a vector format is not 
possible. VRML is possibly the closest to that idea, as it is made of 
"objects", 
but it is not practical for image production.

Do try PovRay with eg 1000 px size, you will be surprised!

I have a not particularly brilliant example at 
http://biomodel.uah.es/Jmol/export-image/exportPNG/



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