I have been using eCtune since Nov. and it has been by far a pleasure. It has a TON of features and the best part about it is everything really works. There have been a couple of bugs (I have experienced 1 personally) but majority have been minor (data playback, saving and connecting issues) but Calvin is all over them and they are quickly resolved.
I have used Crome for a couple of years and I always had issues with it. It took a longtime to get the car running decent and then after a couple of days the car would lean itself out or richen up, I would make changes to the IAT, ECT compensations and it would be fine until a few days would pass and then it would do it all over again. It got to a point where I was actually afraid to leave the house without the laptop. Datalogging would lock up, or miss cells, CEL's ugh I can go on and on. I just couldn't take it anymore and was just about to go out and get a Hondata system and then the whole lawsuit against Dave Blundell came about and I refused to get any Hondata product.
Then I found eCtune. After months of waiting he finally let people start to buy pre-released versions and I snatched it up. Went out to the garage and made a basemap and within 10 minutes the car was up and running and the idle was rock steady. Took it out for some street tuning and after 2 hours the car was running better than I ever got it running with Crome. The car runs smooth as silk, no more of the previous issues I was having and I can go out with the car without having to carry a laptop with me, ah, peace of mind !
As for how it compares to Neptune, I have never used it but eCtune has more features though from what I understand the Neptune software is solid. I also can't compare it to Hondata as I never used it and after the whole lawsuit thing, they will never see a dime from me. If I had no other choices, I would actually switch back to Crome.