The entire diablo 2 economy is rune-based. That said, the reason why Um and Ist are popular trading runes is because, as said above, both have desirable mods. Also they both are staples in many runewords. They are uncommon enough to have trade value, but common enough that everyone has some to trade.
With the advent of the ladder, the massively duped SoJ went out of favor as currency because of its extreme scarcity and resulting extreme price. In short terms, you couldn't make change anymore.
Runes were a logical choice, as they are graduated from common to insanely rare and are useful for the properties they provide and for making runewords. Um and Ist, in particular, fit very well on this graduated scale. They are useful to almost all characters, providing resists and magic find, and they are about as scarce as 1) relatively high end items (um) and very (but not insanely) high end items (ist). On ladder, I would say that pul is the basis for pricing items, and pul also has some characteristics that make it a good choice. It is not quite as scarce as um and it has a special use, mainly upgrading items in the cube.