The Jem's neck is rather thin and flat, particularly that of the DBK, which a JS
has a more rounded, Strat-like neck.
I would say that the neck shape is probably the most important difference between these guitars, but only you can decide which is better, so I'd find an example of each and play 'em before deciding.
++1 I've owned both and still have my DBK. While the Burned stained Blue JS1000 I had was a gorgeous piece, also got it mint when I got it 2nd hand, it stayed that way. A flat fretboard is a must for me and that wat what my RG570 offered me at that time. The round stratocaster-ish fretboard of the JS1000 totally wasn't for me. That combined with the pickups (see lower) made sure the JS1000 stayed in it's case.
Neck thickness may vary, but I prefer it more slender, so I got my hands on a DBK a bit later. Since the DKB is the only JEM with a ultra slender SuperWizard neck, it's a bit a beast on it's own. The industrial finish really is industrial and to me clearly a point where they kept things more affordable. But overall, it has a look of it's own and gives in interesting contrast between the matte relief finish and the flat supergloss mirror pickguard. Up until now it's the best playing guitar I've owned and one of the most affordable JEMs around.
Also, I'm surprised no one mentions anything about the pickups
. The JS1000 has the satriani classical Pafpro and FRED, while the DBK is rigged with Breeds. I absolutely dig Satch's tone, but the FRED didn't work out for me or my rig at that time. The FRED is rather nasal sounding, while the Breeds are (If I'm correct) a crossing between Paf's and Evolutions. Quite versatily, nice bite and harmonic sensitivity and enough power to do some metal stuff.
I'll take a DBK over a JS
every day, but so like others have said, you really have to play both guitars yourself and check it in terms of pickup sound and neck feel. 2 different guitars !
ah and somtehing I don't like in the JS
design: the straight headstock. I prefer angled and have weakness for reverse headstock (too bad not more of these are seen). And as far ergonomics: the RG/JEM have this extra cut out on the back so you don't have a hard edge cutting in your belly