Once my 99 had the hiccuping problem at low rpm. It usually idles at 650, but it was dropping to 300 and hopping back up over 650. This was after a drain on the battery (I had the stereo playing for a while, fairly loud with the car off), and a drive with the stereo on. After parking the car and getting ready to turn it off, it did the hiccuping. I only experienced this once. By the time I got home I put the battery on the charger and it was showing a good level. The alternator must have got it up to normal, hopefully it wasn't too low. I have an automatic so the problem wasn't the clutch, etc.

So if my story's an indication, I would point my finger to the battery, alternator or something in the electrical department.