What's the best modification you've made?

Adding Lindy Fralin's hum-canceling Split-Jazz pickups to my 2003 MIA Fender. Eliminated all the single coil hum, and if anything improved the tone. I've tried five sets of noiseless J-bass pickups across three different basses, and the others were all good in their own way, but IMO these are the best for preserving classic J-bass tone. They have lots of punch, and growl for days. I've had them for 13 years, and they're staying in this bass for the duration.
 
Fender FSR Jazz bass…Super 55 pickups, Audere Z3 preamp, LaBella gold tapewounds. Putting in the preamp and pickups was almost as easy as changing the strings…no soldering required.
Entirely different bass…especially nice if you're not a fan of the Fender preamps and regular noiseless pickups.
Seriously, I should buy a set of Super 55s before they really get hard to find.
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there are a lot of really small things that make a huge difference.

probably the smallest one, with the biggest result, is adjusting pickup height. when they're nice and close to the string the sound is almost always much fuller and fatter with more character and dynamic range.

as far as actually swapping a part of the instrument out, you can't beat replacing a stock fender or similar bridge with a hi mass bridge.
 
Got rid of my Highway One's BadAss II and replaced with a vintage (threaded) Fender bridge. Better overall tone (for me) and 90€ in my wallet, which I invested in an EMG GZR pickup set. Absolutely the best mods I've done.

Ha! I did this same thing with the BA bridge on my 60s jazz. I bought it used where someone had stuck a BA bridge on it and the strings not passing directly between the poles on the pickups set off my OCD. I bought a 60s threaded bridge, swapped them out and have been very happy with tones. I really think it was the string spacing.
 
mods/upgrades: tuners, bridges, knobs, headstock alterations/painting, pickups, electronics/wiring harnesses, side dot alterations

probably the bridges and the electronics have been the most functionally important modifications --- the rest are more cosmetic/esthetic.
 
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When I purchased my MIA Jazz Deluxe, I liked the active tone but when I switched to passive, the output level dropped significantly. It was much lower than my passive basses. I removed the active electronics and N3 Noiseless pickups and installed a set of Lindy Fralin pickups, over wound 8% to get more mids and lows and set it up VT-VT. It sounds great.

I also have an MIA Precision that I installed a set of Nordstrand NP4V pickups. It gave me more of a vintage tone.