Generally speaking, how much would these upgrades to my car cost?

I have an 03 Mercedes C Class

1. My side fender is damaged (the part right above the tire) I'd like to replace it.
2. I'd like to replace my headlights with LEDs.
3. I'd like to get a wood trim for my interior.
4. Some new rims, pretty much any run of the mill rims will do.
5. An MP3 player jack so I can listen to the music from my phone (its NOT an iPhone).

The "upgrades" you desire will far outweigh the value of a 10+ year old C class. If it were me, I'd realize this and look for something else.

I agree with the other answers. The cost will exceed the value of the vehicle which is under $6K. You might be better off looking for a loaded '06 E-class which will be near your investment.

Fixing your fender will bring the value of your car back to where it should be.

Rest won't add any value to it and may even subtract from it. Customizations are risky at best - as if potential buyers don't have the same taste or needs as you, then it's a negative. If you modify your car, do it for your enjoyment. I wouldn't expect anything back.

Adding an MP3 jack may be a problem. Mercedes-Benz uses proprietary system for its audio. I would ask a competent and knowledgeable shop to do the work. Fixing it will be very costly.

1. Depends on what exactly is damaged. If it's paint, dents, or both. If a repair shop can fix it, it will be a lot cheaper vs. Replacing it. Price depends on what shop you take it to.
2. The car doesn't support LEDs. There was a xeon option, but each head lamp assembly costs around $1000. And you'll need two for both sides. You may also need a headlight control unit for the xeon light assemblies.
3. You'll need to get it either at a scrap yard or a dealership. (around $1200-$2200 for the entire set)
4. Don't do that to a Mercedes-Benz. These vehicles are supposed to be a work of art, not some throw around car. If you don't get the correct rims, you can seriously mess with the ESP and BAS systems.
5. The other user is correct. Mercedes-Benz uses a proprietary audio, electrical, and computer system. If you modify it, you can blow the front/rear SAM or the CAN. The SAM (signal acquisition module) and CAN (controller area network). Both operate everything that's electrical and computerized in the car. If you modify the system you run the risk of damaging either components, which will cost several thousand dollars to replace.

As the other users have said, the cost for these "changes" will exceed the value of the car. The repairs will raise the value, but the mods will actually decrease the value.

You seem to be confused. Those items are not "upgrades" (lol) - the first is a simple repair, the rest are distinctly DOWN-grades - except the last (which is a very expensive, dealer-only accessory).

Also, there's NO SUCH THING as "LED headlights" for that car. And for pete's sake, why would you want to ruin the car's looks, handling, ride, safety, and resale value with "run of the mill rims"? That makes NO sense.

You need to rethink all of this. Yes, get the body damage fixed - but the rest of that garbage is just not practical.