Some feature requests/usability bugs:
1) The optimize button shouldn't automatically decide the fate of some files on the disc it thinks are dummies/excess baggage. You could have checkboxes on the "optimize feature" for what to optimize.
I've noticed at least one image (European Gripshift) which has a list of all files on the disc with checksums. Padding optimizations would reduce the size of the image but the game doesn't load if some files are zeroed. I also noticed another game (Taiko No Tatsujin) which doesn't seem to work at all if "Optimize" has been used, but I've yet to confirm why.
2) If I select a file as "Dummy", the optimize button should take care of zeroing it for me (with a checkmark feature obviously).
Now reducing the size of a file I know to be garbage (which isn't detected by dummy search since the file contains random data) is quite tedious: "dummy" a file, save the image, re-open the image, search for dummies, re-save the image. ... you get the picture
3) The "layout" tab should tag or color the files which have been modified during the session.
This helps to detect if for example "optimize" did something I didn't want it to do. OTOH it would also help the user verify his modifications before creating the image.