Here's my 2 cents ....
DO NOT get a super charger .... total waste for the cash unless it came that way factory. I say this because nearly ALL used TRD SC I have seen threads on BREAK down conveniently after the buyer paid the seller and parted ways, for sure within 6 months use. So $1500 for a SC, another $1000-$1500 for a rebuild that you didn't see coming ... totally not worth it. There is a better way, its called don't go bigger than 33s, even then may need to regear.
$200 - Buy a K&N CAI .... awesome for $200 cost. Don't listen to the haters, 99% of who have not actually owned a true K&N CAI. I love mine and it is actually California legal unlike the deckplate mod.
$250 - Pair the K&N CAI with a high flow exhaust like a Borla or Flowmaster. I highly highly suggest adding a Tundra (used) factory resonance silencer directly after the muffler. You will have to go hunting for one at a scrap yard.
$800 - Good tires at size 33" max. I like BFG AT or General Grabber.
$1200 - Sonoran Steel 1.2A lift kit. I cannot stress enough how great a kit this is for the "new guy" in the 4Runner community. It worked great for me and many other members, even many who build freaking awesome rigs (Dirtco) for example.
Also see:
http://www.toyota-4runner.org/3rd-gen-t4rs/101758-**rickashays-ome-vs-trd-tundra-lc-review**.html
$80 - LUND Bug Shield. Available on AMazon. Pics in my thread (and others)
$750 - ARB Bumper. Enough said. Expect to pay $750 - $850.
$200 - PIAA Fog Lights. Worth the money. I've had mine 5+ years. Great company.
$400 - Rocksliders or sliders .... use the search function.
$320 - BudBuilt or Savage offroad front skidplate. You don't need the whole kit unless you are really really hardcore and you can always add the rest years later.
$600 - some badass wheels like proComp or other. I prefer the factory 16" 5-stars (see my pics) or the 17" Landcruiser wheels like in COB's thread. I had mine Powder-Coated.
$1000-$1500 for unexpected maintenance. If you are anywhere near 150k miles or more this is a must. There are so many things that will likely come up by the time you hit 200k miles. I'm at 217k and have owned my Runner for 10+ years now. Check out my thread for details.
$300 - Window tinting, again heres my suggestion: don't do more than 50%. It's cool when you are 20 but down the road (when you realize not being able to see you your side windows at night is incredibly dumb) you may regret the limo (5-10%) tint.
$20 - upgrade your battery (negative) to chassis ground wire to 4G .... like now. Search for the "Big 3 upgrade" --> even if you don't do the entire upgrade just this one cable will make a noticeable difference. I have 217k miles on original alternator and nearly all my charging and battery issues were fixed by this one cheap upgrade. My ScanGauge II now reads 14.2 V consistently.
THINGS I WOULD ABSOLUTELY NOT BUY until I first took care of the above list ....
1) a roof rack. The factor rack is great and 98% of the roof racks drive around empty even on the trails. .... I'm just saying guys (sorry).
2) a winch. A good winch is pretty expensive and probably heavy. Save yourself the $500 and find a friend to wheel with so you don't need a winch.. Great for the semi-pros and pros but MOST 4Runner owners, even those who offroad 5x times a year do not need a winch.
3) do not buy tires bigger than 33" for any daily driver.
GOOD LUCK. Whatever you don't walk into a Offroad Warehouse type of (everything truck) 4WD store and ask for advice on lift kits. If you don't go with the Sonoran Steel than do a lot of reading (here) and purchase your own parts. There are many threads on this but I still recommend the SS 1.2A kit. You will not be disappointed.