What's the best modification you've made?

I put a switch in my PJ like a Tony Franklin sig instead of VVT.
I've always swapped out to VBT for Jazz and PJ, but this sounds much better with the switch.

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HendriX pickups and a BQMusic V12 tone control to my 80's Japanese Fender PJ and J. And a surf green finish plus red tort pickguard for the Jazz. Fretless conversion + Aguilar OBP-3 of my Fender Dimension American Standard. Huge improvement, and it sounds amazing fretless. Remarkably, more like a double bass than I expected.
 
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Took a tired sounding old passive Ibanez RB760, with a small crack in the body around the tone pot (someone dropped it) and a broken J pickup, a missing cover for the electronics, and upgraded it a bit.

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I got a replacement J pickup. I installed a Darkglass Tone Capsule preamp. I designed a vinyl print for the front, and I designed a 3D printed a new cover for the electronics. I cleaned up the fretboard and frets as well. The tone improved significantly and it looks a lot better too. I’m happy with the result.

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Even Doug himself at Darkglass enjoyed the end result when I showed it to him. :)

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After strings, it’s pickups. Single most dramatic change in your sound. After different strings.

After changing bridges a few dozen times over the years, I’ve since concluded changing out a bridge is seldom ever worth the effort or the money.
 
Excluding strings, what's the best modification you've made to a bass guitar that resulted in an improvement to the sound?
I had a set of Nordstrand Big Splits installed in my Dingwall Afterburner at the same time I had a Darkglass Tone Capsule that was installed by the previous owner removed. Awesome bass got even better.

Honorable mention - I did a RWRP pickup mod in my 4003 Rickenbacker. It helped with the hum. I also shielded the pickguard and control cavity with foil, which seemed to have no effect on hum and/or noise.
 
Switching my PJ electronics from a VVT setup to a master volume/master tone/3-way pickup selector configuration was a very worthwhile mod for me. The elimination of the pickup loading effects of the VVT setup was like removing a blanket from in front of the speakers ... noticeably more live sounding. While I gave up tonal options by not being able to mix the two pickups any which way, the fewer tones available to me were better ones, IMHO.

Very nice adition.

Currently I've started a build (actually a "put parts together" build + paint) with a PJ body. I take note of your wiring. Thx!