Rear Storage - blunt force (see Antman's thread for most of these)
De-badge all unneeded emblems (best to do this early for exposure issues)
Rear bumper cup holder
Plasti-dip front and rear emblems
Fire extinguisher
Washers under the front seat posts to change the angle of the seat (Personal comfort)
Drop in K&N air filter
TRD Oil and radiator caps
First Aid Kit
Husky or Weather tech floor mats (Spend the money)
LED Interior swap (some exterior options with this in some bundles)
Sorry for any repeats...this is off the top of my head.