As mentioned before, these are an automatic MUST for me:

Strap-locks: the best $15 insurance policy

Locking tuners: goes without saying

I'm happy with the electronics/sound of all my strats, so no mods there.

And, personal asthetics preference:
I have to black-em-out, because I just love full-on black strats.

I once spent almost $300 modding out a $150 Squire inside-out.
Learned a lot, but I'll never do it again.

I'll just list my favorite mods with any guitar.

One of the first things I do is remove chrome or gold. Chrome is ok on some guitars, but I really dislike gold things that aren't really made out of gold, and I think it looks tacky.

Schaller Strap Locks. Not all of my guitars are equipped with them, but I do use them. Don't ever buy the Dunlop Strap Locks. I've had 2 sets of them fail. They both fail the same way, by wearing out. You won't notice this until they decide to fail at the most inconvenient time. Then when you go to check them, they'll work... until they decide to fail again. It's really quite deceptive and brutal. I've watched my Custom Warwick Thumb bass hit concrete and put a split in my headstock.

Pickup swap. Most of my guitars have EMGs or Super Distortions. After getting my American Deluxe, I think I may try one of the DH-1's in a different guitar.

Bridge swap. Any guitar with a Floyd Rose gets a Gotoh replacement. After discovering this trem, I upgraded all my other guitars. I have 4 Strats that have Gotohs. I'm thinking about having my AmDx converted too. It plays so well, though, I'm afraid to permanently mod it.

I usually play and adjust bridge height to my liking relatively soon after getting a new instrument. I always play my guitar for a few days before I decide if I want to adjust the neck relief... I'll try to get the neck as flat as it can go without buzzing, adjust pickup height then I'll re-intonate. I'll play it for a while and make final tweaks.

I'll only take my guitar to a luthier if there's a more complex neck issue that I can't correct with a proper truss adjustment. If there's complex buzzing caused by fret issues or a badly-settled neck, I'll take it in for a Plek if I want to keep it.

I generally don't do irreversible mods as I do like to keep a guitar mostly stock... though I have no issue replacing hardware components like bridges, trems, tuners and screws with proper replacement parts.

I guess I am a collector... most of my guitars share something similar, they're all one-off customs or really uncommon limited runs... I'm not a girl, but I can understand not wanting to show up at the prom wearing the same dress syndrome. I just like having unique things.

50's wiring is a must for me, with every style I play bar the one my current band play.
Can't be dealing with the treble loss of modern wiring. So all my guitars have that. Aside from that, different guitars are geared for different things. But they all get that, even my Les Paul. A lot of the time, I've found, less is more. Nothing drastic going on (aside from my Tele), just tools geared up to perform best in their fields.

Favourite mod bar non. The blender pot. Seven sounds, any amount of neck pickup in the mix that I want. Easily reversible and no switches.

I strongly recommend the Bill Lawrence Q-Filter to anyone who likes to use their tone control. Couple that with a no load pot and you've a great tool. Usable sounds all the way through the tone pot where you don't lose volume or clarity of the treble strings. Though it removes treble and mids from the sound. Giving an almost acoustic like sound.

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No no and no