From what I can tell my car (KJ2) is missing at idle which is what is causing the rough idle.
I can hear it from the exhaust if I get close to it.

It does so when it hot (first 15 minutes it idles fine).

Miss is non rhythmic.

Very rarely (1% of the time) it idles smooth even after a long run.

About 90% of the time it idles badly.

The rest it idles really badly.

Things changed/serviced/tested to be ok:
Spark plugs
Oil/air/fuel filter
ISC and TB cleaned
All sensors (O2, TPS, ISC, coolant temp etc)
Engine mounts
Idle speed
PCV

Changing the leaking valve cover gaskets MAY have helped the idle. It definitely improved fuel economy by about 10%

depends on how bad it is but mine has never had a perfectly smooth idle and got it at 38000k, now at 150000k. no worse now and it does tend to idle smooth if i've been doing a long run.

Engine condition like poorly seating valves or uneven cylinder compression can contribute.

I could accept not perfectly smooth, but the miss is at times very pronounced.

It feels like I am sitting on one of those vibrating massage chairs which I think goes beyond what is acceptable idle vibration.

Any other tell-tale signs of poorly seating valves or uneven cylinder compression?

Besides the idle, the car runs smooth and quiet

FWIW the KH has had a non-rhythmic very slight hiccup from new. The longer it sits at a red light the worse the hiccup gets until it reaches a plateau and doesn't get worse.
Its like it has a moment where the RPM drops as if its about to stall but immediately recovers. Its very slight in this car and not very noticeable but is there if you listen for it. Back when it was brand new i was concerned about it, but it turned out to be fairly typical of the magna/verada range. Cars now done 220,000 k's and still going perfectly.

Yours sounds like a similar issue only worse.

I haven't noticed it in the KL so maybe they smoothed it a bit in the later models, but the KL does have some slight vibe up through the steering at idle so these cars are not typically perfectly smooth IMO. KL had 25,000 k's on it when i picked it up so i'm speaking here about the behaviour of very young engines.

Thats only my experience in two cars, so if anyone has a different view then please say so.

Thanks KWAWD, it sounds like a similar issue but at it's worst my car seems to have a constant hiccup giving really poor idle.

I've been in a few 3rd gens, some of which had "poor idle" but my car is much worse than any of them.

Had a TH and now a TJ both have an idle that isn't exactly smooth, they both always idle better after a long run and if I was feeling rich 98 octane fuel always made a difference. I think the car's need an "Italian" tune up every so often AKA Full throttle for 60 seconds.....

Bump anyone?

Check your spark plug leads?

Park in a very dark garage with every light off, pop the hood, and try to watch the high tension leads from the plug right back to the distributor.

If you can see the leads arcing anywhere, get them replaced. If they test okay and they meet resistance specs with an ammeter, distributor could be next port of call.

http://m.wikihow.com/Test-Spark-Plug-Wires

$.50 worth - less tax...

Is the timing correct on your car, replacing the cam belt can result in incorrect Cam/valve timing which will give a very bad idle?

Timing belt hasn't been replace for a while (due for one actually)

The standard answer for a rough idle is to clean the throttle body including the idle speed controller. Also adding a bottle of injector cleaner to 3/4 tank of fuel can help as well.

I cleaned the TB and ISC, and though they were quite dirty I noticed no difference in idle