I've got a rough idle that developed when I changed plugs recently. While I had the upper intercooler piping off I noticed that there was considerable oil leakage from the valve cover gaskets--I wiped it up and tightened the valve covers slightly (I'm always afraid of cracking the valve covers or stripping the threads in the head) and installed the new plugs.
Almost immediately I noticed a harsh idle, a stumble, especially when warm. I pulled #1 and #6 since they're easiest to get to, and #6 had been fouled up by oil.
This is only one of many possibilities, but check for oil (or water) around the plugs, and also check the condition of your wires. Also, if the coilpacks have been removed recently, ensure that the grounding strap from the coilpack mounting plate is connected to the head.
Hope this helps some!