A belated wrap up of a poll done here. Before we get started, upgrade here is subjective. Some people feel that parts replacement is heretical because for an instrument to reflect its true worth, the original parts should stay put. Also, what's upgrade to us might not be the case with others.
Looks like the most popular upgrade is a pickup swap. We can agree that this is the most noticeable change to tone but then again, some people can hear the difference, others can't. That aside, the most fundamental agreement here should be that a different output pickup would manifest a different reaction, tonal differences included, for both clean & driven tones. The marked difference could be heard between passive & active pickups. Many of us have treaded this path & we know the outcome.
Capacitor is the interesting runners-up. This had been a recent phenomenon after stores here inventorised capacitors as replacement parts & the fact that we can purchase some easily online. Capacitor swaps are experimental because we know that it's a component that is highly unlikely to corrode or deteriorate. It's also one of the most controversial parts swap because according to the electronic engineers, the different materials involved did almost nothing to tone.
In third position, we have a tie: Volume/ tone parts vs. nut. The thing about volume/ tone pots is that we have to replace them over time due to deterioration; oxidization, rusting, corrosion, you name it. It's inevitable. Those of us who chose to replace them before they expire, now that's experimental as well. Fender dweebs for instance, will tell you righteously that you don't quite possess the Fender tone until you have CTS pots in your instrument(s). Moving on to nut swaps, this occur more commonly with acoustic players. Solid body electric players who are in driven mode most of the time are not too particular about their nuts. Also, whether the different nut materials manifest any tonal difference, is another area of subjectivity.
Looking at the bigger picture, we see the guitar stores here having pickups as part of their inventory (almost but not all stores). We also see stores carrying replacement parts like pots, pickup selectors, input jacks, etc. because these expendables are necessary purchases over time for instrument owners. Subliminally, stores with such spares with them display a knowledgeable front at the very least. It's a platform for technical conversation because instrument care in its basic understanding is dealing with technicalities- which pots work better with which pickups, which guitar polish gives the best gloss, which input jacks are more durable; you get the picture.
To me, parts swap/ upgrades is an adventure & the most worthwhile if we do not let our expectations get the better of us. Also, let's not impose our parts embrace unto others; what might work for us might be the formula for disaster for others.