It's been a while since I thought about this list of basics. I've recently converted to Megasquirt and have had a lot of time to review the Bentley schematics. If it still doesn't run right after you've checked the basics and did the tune-up, replace the following:
Replace with O2 sensor if you do not know the history of the car. A previous owner may have had a bad coolant sensor that caused the engine to run rich and destroy the sensor.
To the same effect, inspect the cat. converter for cracks or chunks while you are down there. This can fail pretty quick depending on the severity of the fueling condition.
Replace the injector harness. At 98K, mine had some bad cracks. This can cause issues if the engine gets wet. The harness can short and not open injectors when you need the fuel the most. A resistance check will not immediately point this out.
A new knock sensor would also be a good investment. Make sure it is torqued properly. Also, keep the wiring away from the alternator and the power wire that feeds the battery. Try to route it against insulating items.
Also, if you know that the timing belt has been replaced, be concerned about the crank sprocket key. The bolt can loosen and strip the key way. This is what you check if you can't seem to get the timing right.
Some people have had their Hall sensor on the distributor fail. I don't recommend immediately replacing it. Have a professional help you trouble-shoot this item. Or if you know an engineer with a USB Oscilloscope, bribe him with beer for his assistance.
If you have hard starts due to a draining battery. Find what item is grounding by using your multimeter set to Ohms. Put one lead on battery positive (+) and the other lead on chassis ground. Pull each fuse until you have more than 300K ohms resistance. Recharge the battery and it should start up good. Find out why that accessory was grounding before re-installing the fuse.
And if it still doesn't run right, consider the possibility of a bent ECU pin. If the chip has ever been replaced, the placement of the ECU makes it hard to get the harness connected correctly.
It's really a pretty basic engine setup. There's not much else to go wrong. (famous last words)