I'd get the relatively expensive (new OEM) but small things that can completely kill you dead in the water or make it dangerous for you to drive. Things you can keep in the glove box or where ever without hurting for space. Things that the dealers don't keep in stock and the parts houses might not either, so you'll be waiting on something shipped, possibly after a tow home.
Get:
-All the 'special' relays from the fuse boxes
-Brake Booster Check Valve
-Mass Airflow Sensor (MAF)
-Throttle Position Sensor (TPS)
-O2 sensors (possibly, if you can prove they're good)
-Ignition coils
A bit harder to fix on the fly, but:
-Fuel Pressure Regulator (FPR)
Cosmetics:
-Stock up on little clips, etc
-bulbs (brake light, reverse, dome light, etc) If you can score bulbs from someone whose done an LED upgrade, all the better
-plastic seat 'feet' covers
-If it's a Limited with power seats, get the driver's side plastic seat cover. There's a clip here that breaks off so the whole cover pops off, adjuster lever with it
Someone mentioned vac lines and that's a good idea. Nothing is a bigger pain in the ass than working on the truck and putting it all back together only to have a 20 year old perfectly bent/molded vac line just snap in half on you. Then you have to make another parts house run (possible in another vehicle) just to get the new line.
'Treasure' from other Toyotas: I know that the MAF from a 2003 Rav4 is the exact same one as the 1999+ 4runner (I think the MAF style changed in '98?). I think I heard that the Avalon fits also.