On my 97 Saturn sc2 I changed plug wires and #3 spark plug. Had trouble getting plug to seat correctly and now it runs really rough. What could be wrong?

check egr valve operation, check iac motor, check for a vaccum leak, what's the condition of the ign wires, plugs etc?

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Are plug wires connected in the right firing order to the plugs? Also are the spark plugs gap correct? Was vehicle running rough before tune up or only after?

try change fuel filter ,air filter ,spark plugs and cables

No, the longer length will not cause your problem. The longer wires are simply for the plugs longest from the distributor cap (or coil pack) to the spark plug, and no particular length is critical, just as long as all wires will fit.
Do you mean it ran fine before you changed the wires and plugs? If so, you may have one or two not fully seated at one end or the other. Go back and make sure each wire is pushed in correctly, You should hear or feel the new wire snap over the new spark plug.

mine did the same thing. Are you SURE you have the firing order correct?? Double Check that because the firing order is from the PASSENGER side to the driver side is....1 2 3 4 ... and on the coil pak from the PASSENGER side to the driver side is ... 4 1 2 3,
I hope this helps!

the fuel injectors can be the cause.first you must isolate which cylinder is shutting down. When the engine is missing pull plug wires one at a time to determine which one does not slow or make engine run worse. CAUTION: use rubber handle pliers or rubber glove to pull wires off plugs.

at night spary a lite mist of water on the coils and see if they spark out,if you see sparks then replace the coils, make sure to clean the mating surface of where the coils and module sit, also clean the area where the module bolts up.

Check to make sure you have not cross the wires and your firing order is off by one wire. 
http://autorepair.about.com/library/firing_orders/bl-fo-8792.htm

Good luck and hope this helps. 

p303 is a cylinder 3 missfire I woul first check the coil and then the ingnition module, Then if this dont work you could have a bad injector. If after testing and still no fix you should check the compression in that cyl.

if you have high resistance in secondary ign. system (plug wires, ign.coil) this will cause this code to set. make sure you are using a high quality spark plug wire set. not from autozone!!! and denso non platinum tipped spark plugs. also use a diaelectric grease on plug wires to keep moisture out.