re: SNES
Another way to do it would be to use tabs, a la
vSNES' scene viewer.
The screen and BG info and the palette, while nice to see, are probably only necessary for ROM hackers / emulator devs. Making them visible only via checkbox / menu option / tab would speed up the game nicely.
(I'd also remove the dropboxes and use only radiobutton groups.)
Using separate windows for each category is definitely interesting, as long as the layout can be saved. (The windows snapping to each others' edges a la Winamp would be nice too.)
Regarding the palette options: AFAIK ZSNES (and SNES9x?) simply shifts the color values 3 digits to the left (XXXXX to XXXXX000), while bsnes uses the topmost 3 bits to fill the lower bits. This "spreads" the colors a bit and makes it possible for a color channel to have the value 0xFF.