stacking used to confuse me too. basically, if a rune provides an attribute that is stacking, you can add more runes to increase that attribute. if it is non-stacking, then you will gain the benefit of only the highest rated rune.
eg. 5 runes of vitae (+10 stacking) placed on various armor parts will give you +50 health. however, 5 suprior vigor runes (+50hp non-stacking) will only provide +50 health; however if the vigor rune was stacking, you would have gained +250 health.
Stacking...
jhu
dargon
as jhu said, however, be aware that whether or not a rune, etc is stacking, any and all negative effects are. So, from jhu's example, 5 sup axes will only give you +3 axe attribute points, but they will give you -375 hp (5*-75)