I had a very similar problem with a eclipse I had. Turned out to be a small leak in the head gasket that was leaking into one of the cylinders causing it to misfire sometimes. I would also check your distributor or coil dont know which one you have. Could also be bad clogged injectors. I dont know how mechanically inclined you are but that would be where I would start.

Of course, i would only move on to my suggestions after changing the fuel filter like BushMasterBoy suggested.

Keep us updated.