For major power upgrades installing a Turbo system or a Magnuson Supercharger (?$8000) is about it.
For maybe
small increases some people advance the timing a few degrees (IME to ~6-7' BTDC in the FZJ80). For the models with a "POWER" button you can leave it pushed in all the time. The engine won't make more gross horsepower but the button changes the transmission shift points to keep the engine rpms up before shifting to the next gear, so a bit quicker acceleration from a stop.
All the usual "tune up" things will help the (Petrol/Gasoline) engine develop it's original HP ie: air filter, spark plugs, distributor cap and rotor, and maybe (if original) install new Toyota spark plug wires. Fixing any vacuum leaks, cleaning the Throttle Body and MAF can help. Having the fuel injectors sent out to be cleaned can also help the engine run efficiently but that's a lot of work to remove those.
Some people may not agree but if you don't want to pull your fuel injectors using one of the newer more expensive high level PEA (containing Amine chemicals) fuel injection cleaners a couple times in a row (or more) and at double strength ie: only 8-10 gallons in the tank can help, IME. Using a Top Tier gasoline may help keep the injectors clean also. It depends how dirty the injectors and valves are IME/IMO, some crud cannot be removed from high mile neglected injectors unless they're sent out to be cleaned ultrasonically. Also you can't "flash" the ECU or install any sort of "power chip".
Toyota parts are best. IME the only exception (to using Toyota tune up parts) are Denso Iridium Power or Iridium TT spark plugs (might add 0.003 HP

). Main advantage is that you can run them up to 100,000 miles, the distributor cap and rotor need to be replaced more often than that however (IME).
Wait for others to chime in.