Amn...It really depends, sometimes I need some more Tir runes for my starting characters with mana problems and sometimes 1 of the lower runes come in handy. Also the 3 "elemental" runes (Ral, Thul, Ort) are nice for mercenary resists if they are using Griswolds armor or something, but if I have a reasonable amount of the lower runes I just leave them. Cubing sucks
Right now, I'm at Tal. But it is likely to go higher soon. I've got 4 of each rune until Lem so I think it's enough safety if I happen to need a low rune and I don't have to pick up some anymore. As many have pointed out, cubing runes sometimes takes more time than the time required to drop the rune cubed and moreover cubing is essentially destroying runes (it's harder to find two Vex than one Ohm). That's why I'm reluctant on rune cubing. Right now, I cube up to Hel rune all the rune I find from Tal to Dol as I estimated these are easy enough to find versus usefulness. I could probably go higher as I might have exaggerated the usefulness of Hel (I like to know I'm able to unsocket items but I actually never have used the recipe), maybe Pul should be my goal with a reserve of something like 8 of each runes from Amn to Lem.
I pick up Shaels, and occaisonally dols, if they aren't out of the way, rune cubing is boring and i have to find the chipped gems also to upgrade, I have stashes full of lower runes that i never use also, probably at least 50 of every rune below shael.
I usually pick up only Tirs and higher, (TIR for crafted Legendary Mallets/thunder mauls), but not allway. Often I am not in the mood to pick up lower level runes, but I allways pick up TALs and higher.