I have run all three, on the same truck, with different setups. I would run a spartan again, if I fell into a deal on one. Great gauge setups, and awesome power. But like was mentioned earlier, dual pumps, different turbo options, etc require custom tuning.
I wont run H&S again. The engine tuning is very good. I like the LOW BOOST FUELING option they have now. I can run a really hot tune, with the fueling turned down, and have tons of power on tap, with little to no smoke, all day long. I recently towed 16,500 lbs behind my 450 with the 300 HOT DAMN tune loaded, with LOW BOOST FUEL turned down to #2, and never had an EGT issue, or poured a ton of smoke out.... And once the TC is locked, it runs great. Problem for me is shifting. Def not crazy about it.
SCT is my tuner of choice. With Eric's tunes. Tranny tuning options are great. Power is everywhere. Smoke is manageable. Only thing is a very touchy throttle on the Xtreme tunes... I have yet to try Gearhead tunes though. I am prob going to give them a run, as I hear good things about them, and I am all about options.