Most of them. But honestly, this was my midlife crisis car, and I really got a great deal of joy and satisfaction out of doing all this crazy stuff.
A much shorter list would be the things I would do again.
The #1 mod I would do again is the tune. Huge difference, easy, no down side.
I would also get the shark antenna again. Cheap, easy, and lets me put a walmart roof rack on to carry lumber without having to worry about an antenna in the way.
I would also plastidip the spoiler and "diffuser" again. Easy cheap and looks good (to me)
And the window deflectors, which let me park with my windows open a little bit and never get a drop of rain? Cheap, easy, effective. I think there's a trend here.
And finally I would get new tires again. But I would spend more time and effort picking the tires instead of just going with whatever the NTB folks reccomended. Still, practically anything is better than the crap the Sonic comes with.
OK, trying to answer the question you asked though... lets see. Lower engine mount. I drove around with that thing on for most of a year before I finally went back to stock. So much better. I know I probably sacrificed some power, but that's OK with me.
And I got an exhaust system with resonator delete. Mistake. Resonator doesn't cost much power at all, probably the least effective delete possible, and all you get from it is a droning sound, no "improvement" in sound output or power output. It's not bad enough for me to go to all the effort and expense of getting in a resonator and installing it... but I regret it.
The rest of the stuff I did, I feel did improve the car, it's just that for the most part, I no longer really care, the way I did. The 1.4T really has all the power I ever use, other than every now and then tearing up on-ramps for fun, once it's tuned.