Saving your money is good advice. How much effort and money you expend should depend on your goals. Do you absolutely need those few tenths of seconds at the track? If so, performance tuning might be worth it. If you've got some aftermarket exhaust and intake hardware, there are a lot of maps out there which can give you a reasonable ride. For me, most riding is done at less than 15% throttle and a good idle and smooth throttle in that range is important. All of the richer tunes I've tried work pretty well at WOT but I don't do that very often. There's usually not enough road where I live.
TuneECU is a good program but you can't change the fuel or ignition in real time with the engine on. So it's tedious even for an experienced tuner to use this program because he can only apply new trims with the engine off. Tuneboy now has tuning in real time but that program costs and you still have to find a tuner who can use it. It also has an autotune feature which works with a wide band O2 sensor.You can also adjust the timing in real time. I believe Carpenter uses Tuneboy.
The Rocket fueling is based on throttle position (TP) and rpm above about 20% throttle using the main fuel F tables and manifold pressure (MAP) at lower TP using the L tables. You can shut the L tables off completely but then you lose the sensitivity the MAP gives you at low TP. The Power Commander has two advantages - it trims the fuel in real time and the trim integrates the MAP and TP based fueling. If you can find a good PC tuner, he will manually create a trim table using all gears over the TP-RPM range. I was about to go this route but I got a tune (20145 Gracie) from Scott (Warp) which seems to be doing it so far. I'm hoping to save the money on tuning and use it for shocks and springs.