Jennifer,
A knocking lifter can be caused if you have a worn timing belt, crankshaft, bad valves, bad valve springs, bad lifter, wrong grade or dirty engine oil, or even dirty gasoline. A mechanic may suggest a valve job, which can be pricey. Do that as a last resort. The cost of a valve job may be worth the value of the car itself.

Simpler and less expensive options to try first would be to get an oil change. Unless you're in a really cold part of the world (Alaska, mid - northern Canada, etc) use 10W-30 engine oil. Whomever changes your oil may recommend you use 5W-30, but 10W-30 is what I use... even when I used to drive my Eclipse in the north eastern winters. After your next oil change, add a full tank of premium gasoline along with a fuel injector cleaner. You can buy the cleaner at almost any store; KMart, WalMart, Autozone, etc... You don't have to buy the most expensive, but that's up to you. Low grade gasoline and dirty fuel injectors can cause your car to perform poorly, and eventually cause a knocking sound. You engine trys to prevent this knocking sound by decreasing your engine performance.

From your description of the high-pitched squeaking noise, it sounds like a problem I had with my own Eclipse. And, in fact, the brakes were the problem. My initial problem was that my calipers were sticking. This caused the brake pads to be pressed against the rotors. This is what causes the squeak. When you apply the brake pedal, you give the calipers a little extra push to release. You should have your caliper glide pins greased up, and have the pads and rotors checked. Depending on how long this has been going on, you may have worn down your pads/rotors enough that they need to be replaced. There are little rubber boots on the caliper glide pins that prevent brake dust and moisture from getting to the glide pins. Over time, those will wear and crack, allowing lots of debris in and causing friction to the glide pins. When there's friction, you get sticking.

Along those same lines, I had a squeaking problem like the one described above, but it was being cause by my parking brake cable. The cable had worn down and would not release the caliper when I disengaged the parking brake. So basically, I would be driving down the highway with one of my rear brakes always on. Not a good thing.

Have you brakes checked, and try the cheap options first for your knocking lifter. Good luck!