If you have good spark from some of your spark plug wires but not others, that is actually a good sign, because it makes it far easier to diagnose the problem.
For most every 4 cylinder motorcycle, there is a coil which fires cyls 1+4, and a coil which fires cyls 2+3.
Therefore, if you are having good spark on 1+4 for example, but not on 2+3, then you know something is wrong with that coil which fires 2+3. Either it is a bad coil, its wiring is bad or disconnected, there is one point or capacitor which is bad(on points bikes), malfunctioning CDI, etc.
For 2 cylinder bikes, you can either have 2 coils, each for a cylinder, or just one coil which fires them both. So if you have a 2 cylinder bike with 1 coil, and you are only getting spark out of 1 of the spark plug wires, then it is a safe bet something is wrong either in the wire, or inside the coil itself. Its a good assumption that everything before the coil is functioning.
Here is a test for bikes with 2 coils. They are interchangeable, so take them out and switch the coils. Now, re-test the spark. If the poor or nonexistant spark follows the coil, then there is your problem. If the poor or nonexistant spark is still on the same cylinder, the problem is not in the coil, but before it further up in the electrical system.