Guess that's a possibility and it's fairly common, but it usually only happens when it rains. Being that you already changed your fuel filter - if you're injectors were clogged, you'd be sluggish all the time. My first thought would be igntion. I don't remember exactly what you did, but here's what I'd do.

1. Check the timing - it's not fun, but a few minutes with a timing light sometimes works wonders. Even though I had a pro do my timing belt in my old 95 Probe SE, the timing was off just slightly and it exhibited the same symptoms.
2. Check spark plug gap and/or replace plugs
3. Check and/or replace wires
4. Check and/or replace distributor cap AND rotor.

If you've gone through all of the above, it's gotta be fuel or sensors. Check your O2 sensors visually and replace them if possible. If you've gone through all of that and the problem persists, I guess it might be the fuel system. Honestly though, fuel system problems are usually consistent. If you've got REALLY dirty injectors, the car will be sluggish all the time. If it's a bad fuel pump, you're car just won't run or stay running. A dirty fuel filter can be a little more intermittent, but you've already replaced that.

Good luck.