I have used the PC(from DynaJet) III and V, the TV-3 autotuner from Terry Components, and the Cobra Fi2000 PowerPro Autotuner....
My pick of the litter is the Cobra. I am running it on my V-Rod now, and have already received the one I will be putting on my Breakout. I'm not a "tweaker" like some of the folks are that like to play with fueler settings through their laptop, and modify the stock ECU map to match their modifications perfectly.
I prefer the set-and-forget approach, which is why I like the Cobra. It only tunes on acceleration and modifies the fuel release based on that. When cruising it sends a fixed fuel rate into the system. The difference in power and throttle response on my V-Rod compared to stock is like night and day, so the auto tune route more than meets my needs.
Other reasons I like the Cobra is that it will adjust to any modification changes I make and also adjusts to changing altitudes(I ride in the mountains quite a bit every year). So I don't have to load or change existing mapping through a laptop or on the unit itself.
Finally, the Cobra unit does not attach to the ECU connector on the bike at all. So, if I ever experience some type of issue with the motor(hesitation, hard starting, etc), I simply remove 4 easy to locate connectors(2 on the fuel injectors and 2 on the o2 sensors), and the bike is completely stock......
There are a mind-numbing number of players out there for sure and everybody has their favorite!