I think it depends who you ask. I generally stop around thul, amn. But always keep some extras around just in case. You could stop sooner than that and collect Ral's and such and after about 40 of them go and trade them away to crafters.
I keep all runes, even the Els. Always keep one of each and cube up the rest to rals and use for crafting caster amulets (or trade to crafters). Save all Orts as is (for rep. or for crafting hitpower gloves). I cube so that I have roughly the same amounts of Thul/Amn/Sol/Shael lying around, all handy runes. Making stashes of spirit rune sets (Tal, Thul, Ort, Amn) is also a good idea if on ladder.