Why is my 1999 VW Passat Wagon shuddering and failing to develop full power?

My 1999 VW Passat wagon, four cylinder, has a flashing "check engine" light. The engine shakes the entire car and fails to develop full power. I suspect this is some sort of timing or ignition problem. Any ideas?|||take it to advance,zone or oreilly auto pts for free scan...duh....ever been tuned up in 8 years???doesn run too good on 3 cylinders does it!|||Are the spark plug wires all the way on the spark plugs??