Bit over a decade ago, when I was still a naive wild-eyed idealist blissfully unaware of anything realistic about people at all, I set up the foundations for most of my sci fi/fantasy/etc fictions. The piece of supertech I immediately had to nerf was technology based around a form of space compression--somewhere between the MCron Crystal (Marvel) and Dynocaps (Dragonball). And today, I'm still coming up with more reasons to nerf it heavily, to the extent that the civilization based around this technology must certainly have had a shady counsil of vagueness who developed a limited-scope AI to control production and block any of the scarier uses. This after I tied it to FTL capabilities (I'm trying very hard to prevent this from turning into timetravel, not that I'm too afraid to abuse that option for a crisis crossover or something).

It took me much longer to realize how much nerfing of powers unrelated to the above tech I needed to do, partially because I was trying to avoid breaking the laws of physics too horribly (this universe runs on a sort of mangling of GR and M-Theory that assumes fundamental forces each get something resembling a dimension, and that attempts to break the light-speed barrier have lots of wide-reaching consequences).

A few things I've had to seriously remodel (mostly for the sake of in-universe physics not breaking, though I'm sure there are obvious uses/flaws here I've missed):

• Light manipulation. The version I started out with was written as superweight (tvtropes) type IV, when the applications I had in mind were more indicative of a potential V or VI. Since tried to tone down so that this character hovers between II and III (the distinction is a little vague), but I'm sure I'm still underutilizing this character even with all the restrictions I've added. (Invisibility, holograms, filtering specific wavelengths to minimize radiation risks, screwing with radio communication, sometimes can weaponize directly with lasers and x-rays and such).
• Gravity manipulation. This one perplexes me most, even though it seems like it's become relatively clear what limitations it should have--denser matter is more easily affected, sources of gravity can be boosted or reduced on specific objects, all within a finite range. Not precise enough to simulate telekinesis, yet I feel like I'm missing some crucial issues with this power.
• Variations on "interversal connections"; that is, we have a multiverse that would take too long to explain, but spaces or objects in universes can remain connected, after a fashion. These are generally unstable, so those that we see are generally related to intelligence, just because intelligences can find ways to maintain them. The broadest versions tend to catch any high-energy particles entering the affected area and replace them with particles from the connected universe (so if you shot a stream of gamma rays at one of these, you'd get a small amount of hydrogen out of it). These can become more specialized until we have people that can summon and manipulate stellar matter (these tend to be the scariest mofos around, and get appropriate attention from any governments who learn of them), or in some unique cases, people that can "turn into water" (or rather, swap with a mass of water in the connected universe), generate ice/magma/metal, etc. It hasn't really come up yet, but I expect that special relativity tries to be conserved after a fashion, with matter elsewhere being fed into the power-supplying universe, and if anyone measured the delay, it would turn out as one would expect given distances involved.
• I had nebulous "ki power", which I've since remodeled as being related to a unique sort of substance that I'm pretty sure would turn the first quantum physicist with appropriate equipment to study it into a god. However, I only realized that god part very recently. I don't think I can explain it without a long trek through my mythos, but things we've seen related to this substance (and its even scarier source) include: walking talking skeletons (can produce the stuff as a byproduct of feeding on organic matter), people with the most intense exposure becoming effectively immune to aging but with continually degrading cognitive function (and as a bonus, they can pretty much ignore gravity and wind resistance exactly as much as they want), lesser exposure has been associated with abilities such as fireballs, limited flight/hovering, some degree of pyro/electrokinesis. And the ability of the substance to replicate, of course.
• In a completely different direction, there is a more fantasy-esque universe with souls, gods, and magic as facts of nature, except this is part of the same multiverse as the above, so I realized that the laws of physics couldn't be all that different. So I had the creator-god (effectively a backup of a pre-scientific human mind with way more resources to devote to naive conceptions of wisdom), reallocate the weak nuclear force to manage souls, and the sun god (or rather, the superintelligence the creator built to handle the finer details of physics) having a more reductionist/lifist stance. Shenanigans ensue, which resulted in me realizing that, if one of this world's souls wound up in our world, it would turn into a transmutation bomb. Commence panic when I realized that I had a character that I really like getting stuck in one of the more Earth-like worlds in desperate need of a soul-shield, less all the neutrinos give him soul-cancer before all the surrounding gases get zapped with a pound of W and Z bosons and start the biggest Fluorine explosion ever. On the "bright" side, I can now have a supervillain summon the dead from that world and use them as transmutation bombs whenever I need something sufficiently horrifying.
• Oh, and I keep glossing over wind manipulation. It's treated as simple and boring in-universe, when it probably shouldn't be. I'm sure if I did some number-crunching, there'd be a lot of scary possibilities here that I've overlooked. The character who specializes in this can use it to fly and may or may not be able to summon hurricane-force winds or stronger. Most other examples are much more mundane; the most impressive demonstrations are some directed gusts being used to push people a little. Combine this with the first two (light and gravity), and the space program might get considerably cheaper.

In all of this, I expect I'm missing something world-breaking that half of LW would notice within five minutes of having the powers explained (or maybe just introduced--do you need to know that someone generates his fireballs by burning in a weird chemical unwanted bodyhair (and subdermal fat when that runs out) to think of issues that arise from someone with the power to toss fireballs around?).