I hear a loud knocking on the passenger side of the engine. it doesn't start until I put it into gear. It sounds like my engines going to fall apart but it is by the belts.

putting it into a gear and hearing a knock indicates that the engine mounts or transmission mounts are broken
naturally if you put it in neutral it will not move as that what neutral is
perhaps the neutral position needs adjusting as it may still be in drive
have the fault codes read to determine any sensor/servo/solenoid faults before spending big money on a transmission

Well lift the car up and put it on drive wile you can hear what the knock is. See if is your engine or the transmission. And if ok check your spark plugs make sure you getting fire to them

If it sounds like a rapid tapping (like someone is using a small hammer to hit the engine block really fast) then you probably have spark knock. It happens to older engines. As the engine gets older, carbon builds up inside the combustion chamber and effectively increases the compression ratio. Since you are using low octane fuel, it doesn't resist spark knock as well as high octane (this is a reason performance cars use high octane) and thus you get spark knock. An easy way to tell for sure it to run a tank or two of 91 or better octane through. Since you'll be mixing it with 87 octane, it could take two fill-ups to see a result. If the knock goes away, then you know it is spark knock. If not, or the knock I described is not what you hear, then I would need a better description (perhaps a video) of the sound you hear. If it is spark knock, you can run a cleaner through (Sea Foam works great) the engine and that usually fixes spark knock. Sea Foam works best when given to the engine through a vacuum line. Don't add too much at once, it will hydro lock the engine. Just let it **** in a bit and when the idle comes back up, put a bit more in. I would pour half the can in the tank and feed the other half to the engine through the vacuum line. Be prepared, when you feed it to the engine through the vacuum line, it is going to smoke a lot until it burns off the Sea Foam. That is normal and will go away after a short drive.

You may have damaged the engine. So that being said either a bad rod bearing or other issue may be something needing to pull the engine. How is the oil pressure. A rod knock is east to hear. To faster the rpms the worse the sound. Rebuild or replace.

If it knocks when you go from Drive to Reverse or Park to Reverse than its usually a rear engine mount, Bushing or bolts to engine cradle under engine near firewall in center of engine bay towards passenger side. This is for a single or tourqe knock Which means the engine rotates too far and makes contact with a part of the engine bay it should not, or it is loose enough to make the sound.

Easier to notice in a stick shift car than a automatic test by setting Ebrake and putting car into reverse go from drive to reverse in idle with foot on brake if its knocking only when you go into gear this is the problem.

You have a rod knock. Do not drive this car until you have this looked at by a professional. Drive this car and the engine may self destruct.

See if you can bounce car and replicate the noise. If you can, you should be able to find it, and put your hand on it. Stabilizer bushing are a place to look, both at the lower a arm and on the frame. If you narrow it down to the strut, it will need to be replaced. The front trans mount also goes bad, try putting it in drive with your foot on the brake and give it some gas and see if the engine moves an excessive amount.

Check the idler and tensioner pullys for your serpentine belt. I suspect the whining noise heard earlier was due to the fact one was getting a bit stiff or rough turning. When you gave it that extra fuel, the sudden load may have finished it off. Sometimes they lock up, and sometimes they fall apart. Check those items first.

this can be a serious problem, sounds like one of your engine valves, has the car overheated recently? if your valves bent, you need to take the engine apart hope i helped

rcaf arrow: The clicking sound id probably your starter solenoid. Tis solenoid is actually a relay that connects your starter to the battery so the starter can turn the engine over to get it started.
Try knocking the starter with a hammer, (not real hard, just kinda medium) and see if that makes a difference  I suspect your starter is going bad.
Any indication of prior problems with starting?????
Loringh