well i don't know for sure, but i'll relay what my mechanic said when I asked him the same thing about my M800.
Performance wise, the best bang for the buck is sprocket adjustment. In second place, an aftermarket exhaust, K&N air filter, and dynojet. So if you've done the sprocket thing, you should save for some nice slip ons like sil motor (i've got carbon termi's myself) and THEN dyno w/ a K&N air filter.
He said dyno-ing and getting the air filter without an aftermarket exhaust provides some benefit, but he strongly recommends waiting for an exhaust system.
So in short, you'll get a small boost w/ the stock cans, but a very respectable boost w/ aftermarket.
Again, this is just what he told me. He could be wrong, but I thought you'd like someone's opinion.
hi jamsfera, didn't you e-mail me the same exact question? i have done jet kit with stock exhaust and it helps a good bit. on the carbureted bikes, the carburetors are worst restriction, then the heads and mufflers are tied for "Worst". then with aftermarket slipons, the heads become the choke point...
anyway, i don't really like dynojet brand jet kits. they're too dang rich. it's like dynojet just threw a needle in the kit and then ensured that the bike starts and idles and then declares it a successful product. i like the "factroy pro" brand jet kits much more. they're actually developed and tested and somewhat refined.
with dynojet kits, i always advise for the customer to leave the stock main jet in the bike and then install the jet kit per instructions. well, unless dynojet STILL hasn't updated the part about setting the mixture screws... they need to be at 4 turns from seated initially... not 2 turns.
about the M800... it's a completely different animal and any fueling advice about it does not directly translate to the 600. further, a ducati dealer typically is not going to want to talk about non-Ducati brand parts. so they'll be more prone to recommend against the Power Commander. note that the 800 is EFI and the 600 is carb'd. so the 800 gets Dynojet's power commander fuel calibration device. this alters the fueling by "Tricking" or "lying to" the ecu and getting a different mixture as a result. i have good hopes for dynojet... initially, they seemed to be having issues but they seem more than acceptable now. someday, i need to get one and try it out.