My personal choice - divine, magic, electricity. Physical damage types aren't good, sonic is also resisted quite often, skip fire because of flame weapon.
If you aren't going to appy legendary metalls (why bother then?), then also positive is good.
add: I forgot to add acid, it goes after electricity in my rating. But, keep in mind, there is a runeword (quite cheap) that adds 2d8 acid to short swords, daggers and kamas iirc.
And so, here is my final top:
1) divine, magic (and positive for none legendary metals weapons, offhand maybe)
2) electricity, acid, sonic. (sonic for melee only, obviously) (also cold for none legendary metals)
3) anything else, phys. damage types are quite often resisted, same as negative. Fire - resisted and you can have it from flame weapon.
Magic is impressive, but now Minsc leads! Swords for everyone!