From what you describe you have a serious misfire. With the weather getting damper now, any poorly insulated plug caps/coil packs will be manifesting themselves in similar ways resulting in the problem you may have.
Have a listen around the top of the engine whilst it is running. It is possible to hear high tension sparks jumping to earth sound like a crack. Alternatively running the car in the dark helps you see any unwanted arcing. I know that this method is somewhat restrictive when a coil pack is fitted but you can hear arcing.
Assuming to have a misfire as a result of lost spark, be careful not to run the car too long as any unburned fuel will enter the cat and destroy it rather quickly. It can get so hot as a result it can even cause the underseal to catch fire. If it is a misfire as a result of poor spark, that a look at the cat when the car is running at higher RPM, it will be glowing orange.
If you suspect a misfire and can get to the leads, remove them one at a time. If the idle is not affected when you disconnect a plug lead then you know which cylinder to be looking at. Don't do it for too long as more unburned fuel will end up down the pipe. Remove the plug and test it out of the cylinder.
With on plug coil packs I have a set of extensions made up to help diagnose such problems, but most people won't have the luxury of this.
If you have spark on all and all plugs tested, try disconnecting the injectors one by one. I have given you this advice because I can only guess what is happening by your description.
However, there are various other causes that can cause 'rough' running but invariably the ignition components are the cause on these french things.
