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You cant put other runes on a great weapon.
Putting say, a rune of cleaving on a mundane great weapon will only make a hand weapon with +1 strength. If you use a Master Rune of Kragg and Rune of Cleaving you have a Great Weapon with +3 Strength.
I personally dont use it too much, but 20 points to make a weapon magical is not too bad, considering things like etherial stuff and slanns can only be hurt my magic. Its also only a few more points to make it flaming
Current painting project: 2300 pts of Dwarfs in 5 weeks.
Yes, it makes the great weapon magical, but ANY rune on a weapon makes it magical. The point of the rune is that you must place it on the great weapon before you can put anything else on it.
If you put a rune on a great weapon, it loses all its original properties ( hand weapons do too, no parry bonus ) like +2 strenght, always strike last, 2 hands to use. If you want to keep those properties ( the strenght bonus ) you need to use the M. rune of Kragg the grim and only than can you put other runes on it and still have the great weapon bonus/penalties.