AC aside... it's certainly not your problem: Sounds to me like something is either intermittently wrong with a sensor, or you have a vacuum leak. Your ignition stuff works optimally for about 30k miles. Wires usually about every 60k.
1. Check all your vacuum lines. (Free)
2. replace spark plugs (NGK's are only $6 here for 4 of them)
3. replace ignition wires ($35)
4. replace distributor cap and rotors. ($29)
All a tune up is... is 4 properly gapped spark plugs (of the correct kind), a new distributor cap and rotor, and a new set of plug wires. You need a phillips head to change them. Do one plug and wire at a time so you don't confuse the firing order.
If the problem persists after a tune up, it sounds to me like you have a fuel mixture problem. Your car's ECU constantly tries to change the fuel trim based on what the sensors read. Too rich, and you lose power. Too lean and you lose power.
Sensors that cause what you describe: (TPS) Throttle Position Sensor, (IAT) Intake Air Temp sensor, Purge Solenoid and (MAP) Manifold Air Pressure Sensor.
TPS: Tells your ECU where your foot is on the gas pedal so it knows how far open the engine's choke is opened. If the resistor in it is bad, it will occasionally tell your ECU that your foot is NOT on the gas, thus making it add NO fuel to the trim. Bad. Running lean kills engines. You can check it with a voltmeter by piercing the wires coming from its connector with a voltmeter. With the engine off and the key in the "Ignition on" position, it should read steadily from .35 to 4.5 volts.
MAP: Make sure there are NO vacuum leaks. This sensor is used by the ECU to guess how much air is flowing through your intake based on the manifold's pressure. Notice I say guess... Civics don't meter air, so they rely on several sensor signals and it approximates what it needs. Usually this makes you run rich. See any black smoke coming from your car lately? Check the MAP sensor. Usually it's either screwed down to the throttle body, or mounted on the firewall with a vacuum hose leading to the throttle body.
IAT: measures the air temperature from the intake manifold. Depending on what it reads, it trims the fuel rich or lean to aide fuel economy. Varying temperatures affect the density of air, so the fuel mixture has to change in order for the car to run in all kinds of weather. The IAT sensor is usually screwed or bolted to the intake manifold. Some b-series engines have it on the intake.
If your car isn't throwing check engine lights, then check your purge solenoid. The vacuum connection for it plugs into the back of the Intake manifold usually. If this thing comes undone, your idle RPMs will rise to like 1500-1800, it will make no power when floored, but at part throttle it will be hit-or-miss because of the vacuum leak.
I'm not going to even bother reccommending a o2 sensor. That's used to double check what the ECU said to use in the fuel mix, but at 48,000 miles, you shouldn't have a problem with that.
Often times, people do something in their engine bay, and accidentally knock a vac hose loose. I did when I cleaned my engine. I drove to Atlanta and back with the purge solenoid disconnected. That was bad. The car's fine, though. It threw 3 codes simultaneously after about 1300 miles like that, and none of them were related to the problem. It was once again... guessing what was wrong.
jeterkm02: I bet you the CX label off the back of my hatch that your purge solenoid vacuum hose has come lose.