This is how i did it.
I started with removing all gear that could increase my damage with anything but mainstat (weapon, offhand, +%skill dmg, +%elemental dmg, crit and so on). I bought 1 ring with 26 max damage and another ring with 26 min damage. leaving me with 880 intelligence and no other dmg increasing factors
Next i needed to find out how much 100% weapon damage for my character is. I did this by using magic missile and seeker rune that does 211% weapon damage. Now every attack i did was between the ranges of 580 and 600. So averaging 590 divided by skill increase of 211% weapon damage, equals 280=100% weapon damage (590/2,11=280)
Next to find out how damage frozen orb does. First thing i did was figure out how many times frozen orb could hit an enemy. By watching the damage number i found out it could hit an enemy 2 to 3 times. The first time it deals damage is if the "orb" whilst in air passes through an enemy. The second when the orb explodes. The third pretty much directly after it explodes without any visual cue. So if the enemy isn't standing in path of your orb or isn't directly pierced you will deal damage to it twice and if it does three times.
So this is the damage the orb did after extensive testing. 1st hit: 725-740. 2nd hit 1098-1114. 3rd hit: 349-355. Now by dividing this by 100% weapon damage (280 damage) we find that the 1st hit does 260% weapon damage. 2nd hit 393 % weapon damage and 3rd hit 125% weapon damage.
This means frozen orb deals 518%-778% weapon damage depending on how you hit the mobs. Now i did try the same thing with arcane orb with the rune spark and it does hit twice but for 174% weapon damage each time equaling to what it says on the tooltip (349%)
EDIT: After suggestion to redo the test with only the minimum damage ring to avoid damage variation i got the following results that concludes the same fact:
Okey, results from only using min damage ring (rounded off some numbers)
Magic missile seeker damage =459 no variation
100% weapon damage= 217
FO Tooltip 393% weapon damage
1st hit: 570 damage = 262% weapon damage (no variation)
2nd hit: 855 = 394% weapon damage (no variation)
3rd hit: 279 = 128% weapon damage (no variation=
Total 784% weapon damage (392%x2 very close to exactly double, most likely off because rounded off numbers)
Arcane orb spark rune Tooltip 349% weapon damage
1st hit 380 = 175% weapon damage (no variation)
2nd hit 380 = 175% weapon damage (no variation)
total 350% weapon damage (close enough to tooltips 349)
EDIT2: Someone said i should try how it works on a big enemy like Azmodan to see if it can hit more times. My first test where on act 1 zombies but i just did an Azmodan run and it works exactly the same. Azmodan can be hit 3 times by FO for a total of 758% weapon damage