1999 Lexus ES300 - The car has 134,000 miles. When driving it cuts out then a few seconds later will kick back into gear also runs very rough when stopped at a light.

SOURCE: 1999 lexus es300

This has been happening to my car as well. It typically happens when your oxygen sensors start to wear out. Mine does it once in a while and I have the local auto store reset it. Go to your nearest auto store and have them tell you what code it is and ask them to reset the OBD so the light goes out. If the light comes on right away and the code has to do with your oxygen sensors, have them replaced. There are three, two are easy to replace, one takes some effort as it is in a tough to get to spot. The dealer will charge you a fortune to replace them so do it yourself or through a local mechanic. It is a very simple task other then the access.

SOURCE: Have a 1999 lexus es300.

If you have some common tools the knock sensors are no big deal.  If you take a lexus they will make is sound like you need to completely disassemble the engine and scare you off.
First, do you really have a problem with preignition causing real knocking due to carbon buildup, or diluted gasoline or do you have failed knock sensor(s).  Try to decarbon the engine first.
There is a technique used with water being sprayed into a warm engine intake.  This will clean up the valves and carbon buildup which can result in engine knocking.  

The job will be a couple hundred for the parts and a couple hours of your time.  After you are done, you have entitled yourself to approximately $500 in new tools for your tool chest since this is what Toyota and Lexus will charge to fix (about $1k+).

You will need to buy the following to address the knock sensors and a couple other items while you're in the neighborhood.
- 1x upper intake plenum gaskets - 2x lower intake plenum gasket - coolant bypass hose found in the same area as knock sensors - 2x knock sensors (bank1 and bank2) - short pig tail cable which connects both knock sensors to common wire harness. - toyota antifreeze  (2 gallons, if i remember correctly... when mixed to 50/50 (antifreeze/ water) you will have 4 gallons.
drain the radiator drain the front of the engine using the engine drain plug - this plug is on the front right side facing the engine, behind the right hand exhaust manifold. (this will lower antifreeze enough to avoid dumping antifreeze all over the engine later) remove the air filter box remove the connections into the throttle body remove the cable from the throttle control remove the upper air intake plenum remove the two lower air intake plenums remove the antifreeze fill port
Knock sensors will be in the valley between the lower intake plenums.  You will need to remove the rubber antifreeze bypass hose (little short hose blocking access to the knock sensors).
By the way, the reason you bought a replacement, is that if this short hose splits from normal wear, you need to spend this money and effort to reach it, so just do it now.
The little pig tail cable which connects both knock sensors to the wire harness is said to cause a big majority of the problem due to the plastic getting hot and brittle, falling off and shorting to the engine.  While in this mode the engine thinks knock is occuring and starts to retune the air fuel mixture to get rid of the knock until it goes into minimal operations mode.
After replacing the knock sensors (and tighten to torque specs), replacing pig tail cable, and reinstalling your new short by pass hose.  Replace the lower gaskets, antifreeze fill port, lower intakes, upper gasket, upper intake, air intake, air filter, reattach everything, reconnect all the rubber lines you pulled off, make sure there are no splits in the air intake passage anywhere, retighten the engine antifreeze drain plug, and the drain on the bottom of your radiator, and your done!
Don't forget the easy stuff.  Dilute the antifreeze with water and fill the radiator and overflow tub.  Run the engine for several minutes until its hot and opens the thermistat to allow antifreeze into the empty engine cavities.  Turn the engine off and get a cold one as the engine cools.  Once absolutely sure engine is cold, refill the radiator with antifreeze and refill the reserve tub.  Do this at until all the beer is gone and you are both full of antifreeze (in one form or another)..... obviously red stuff in the car, amber down the gut.

SOURCE: 2000 Lexus ES300 - 45K

Are you sure this is a rattle or is it more of a creaking noise? I have a 2000 ES300 and had an issue when I would go over speed bumps and the noise would drive me nuts! However replacing the bushing in the top of the strut mount is expensive due to the labor involved.. Replacement of the strut or the bushing isn't necessary. Just open the hood, locate the strut housing and you ll be able to see the black rubber bushing in the middle. Obtain a can of Heavy Duty silicone aerosol spray and attach a straw to the spray tip. Using a flathead screwdriver wedge the screwdriver between the top of the bushing and the metal pushing the screwdriver all the way to the edge of the metal underneath the roof of the metal housing. Then pry the edge of the bushing away from the metal housing so that the top of the edge of the bushing exposed and stick the straw end of the silicone into the spot and spray generously. Only slight bushing movement will be obtained as the bushing is pretty stiff but it will be enough. Work your way around using this technique until you get the spray fully around the bushing 360 degrees getting it into the area between the edge of the bushing and the metal. Then spray the silicone onto the top of the bushing filling it all the way up until it spills over the metal. After it drains down, repeat again making sure you fill it above the rim of the bushing so it seeps into the area between the bushing and he metal housing (or frame) because this is where the rubbing is taking place that is creating that awful noise. Repeat on the other side and your done. The main goal is to get the silicone into the area between the metal and the bushing along the edge. This happens to be the way I was able to do it. This totally solved my problem and now the car is so quiet there aren't any knocking, creaking or rattling noises. This was a hard solution to explain without visuals, hope you can follow. This will work for sure. The Heavy Duty Silicone spray I used was manufactured by CRC and I bought it from Walmart.

SOURCE: 1999 lexus es300 how to find cylinder no.3 and 4 ?

the front bank is bank 2, the rear one is bank one. The cylinders go from the timing belt side to the right. So 3 is the middle on the back bank, and four is the middle cylinder on the front bank. They are both in the middle so just replace them.

SOURCE: Problem w/transmission Lexus ES300 1999

Is your O/D off? There should be a light under your speedometer, if it says "O/D OFF" than your car wont go to fourth gear. You can turn the overdrive back on on the knob that changes gears, theres a little button on the side. Press it and you should be good.