@Jazz-Cat : I'd break down mods into : Sound, feel, reliability/giggability and looks.
Sound : Pickup upgrades, wiring mods, certain setup mods (E.g. setting blocking out the trem), setting pickup heights.
It's a personal thing - you've probably got ceramic magnets in your pickups, tend to be a bit brighter, with slightly brittle tone. Alinco magnets tend to have a smoother, mellower sound. Not all brands are similar, you can get single coil sized humbuckers, P90's etc...
I've had a cheap ass set of ceramic pups and have had a few different alinco pups (inc noiseless kinman's) - just because you paid big $$$ for pups doesn't mean you'll like them - I've reverted to my cheap n nasty, super microphonic ceramic pickups because I like the dirty lofi-ness of them. That said, the Squire Classic Vibe pups are well regarded as good alinco pickups with a strat-y tone.
Blocking the trem (aka hardtailing a strat) worked for me - I thought it thickened the tone a bit. Noticed this on a few strats.
Wiring mods : I've had a few, the treble bleed on the volume is a must do imho. I also really like the blending the neck pickup with other positions (aka gilmour mod), I don't use it often, but I do like having it available as a option.
Feel : Rolling the fretboard/fret edges, string gauges & pro level setup
My strat feels great (I am biased!), I've rolled the fret edges and fretboard and it made a world of difference. I like a taut string feel so it's elixir 10's - 9's feel too floppy to me and 11's a bit too much like hard work. I like elixir's because they last forever - YMMW.
A proper setup is real important - relief, action, pickup height and a proper string radius'ing will make your guitar feel goooood.
Reliability/Giggability : Graphtech saddles, nut, string tree's, strap locks, shielding, locking tuners
A lot of mods I did (unknowingly) were for giggability. Which is exactly what I have not done with this strat (haha!). Graphtech nut, saddles & string tree's and locking tuners - tuning is smooth, predictable, I hardly ever break a string and string changes are quick n easy. Not necessary for jamming though.
Looks : Well...that's entirely personal and a great attraction of the strat. It's plain jane, but you can do sooo much with it and generally it'll look cool.
Jazzman105 @Jazz-Cat just be sure to make peace with the fact that you generally don't get your value's worth when eventually selling an "upgraded" guitar.
Very true! It might make it more appealing than a similar (but stock) guitar to a buyer who's looking for something that's got those mod's. But usually, for resale, I'd keep the parts stock.
@Tuckstir Nice find! - I've had about half of those on my strat (and undone many of them ?). The two I'd definitely do again - block the trem and put a treble bleed on the volume. The other thing I havn't done yet, but really should is properly shield the cavities - my strat is quite noisy with RF.