I love my s300, honest to god, I wouldn't have half the car I do now if I didn't have that ecu. I didn't take any classes, and I wound up with a car that's almost double the original horsepower (your results may vary) for less than 3 grand if I did it all again. (It cost more than that because I learned as I went. 20/20 hindsight.)
Having never dealt with ectune, I can't speak too much about it. I looked at it, and some of the options almost made me want to reinvest, but as I said before, I was locked into hondata's system.
Hondata's s300 is more designed for people who constantly tweak, tune, modify, and change things around. ECtune is a traditional chip-based system, that feels like it's catored more to tuners, and people who don't want to change their tune nearly as often.
I haven't boosted my car with s300 management yet, but whenever I get back to Germany I plan on tossing a t25 on it. If you stick around, you'll know how that goes. I tuned someone's b20/b18 frankenstein with a t3/4 and it turned out pretty well. THe boost control is nice, and it acts like a factory boosted system, just with less burning rubber.
Both are competitive at this point in time. Hondata's system is more money upfront, but with ectune, you'll probably spend just as much in the long run. If I did it over again, I'd still use hondata's product. I'm a believer.