As a follow up to my can I still dupe the hell out of Diablo 2 runes/gems, which I intended more for the single player fun factor, I am curious to know if there is a well developed strategy for obtaining gems and runes without duping?
This is focused primarily at playing online, on battle.net, but not necessarily exclusively. If it's a good strategy I'll likely try to perfect it in single player first.
Kill the Countess in the tower under the Black Marsh. Over, and over, and over, and over, and over.
She can't drop the very highest runes, but she can drop some pretty awesome ones. For the highest runes, you'll want to kill Baal. His rune drop rate is much lower, but it's still your best bet.
When first killing Countess on Hell, the highest rune that can drop is Lo. Every time after that, the highest rune she can drop is Ist. She'll pretty much drop runes every time you kill her (very low chance of getting no runes). Baal on the other hand can drop all of the highest runes, including Zod (which I believe is a rune that can only be dropped in Act 5 Hell). From Kotsu's comment
The monster with the highest probability of dropping runes is the countess in Act 1 (Forgotten Tower). I think she even drops at least one rune every time. AFAIK Andariel and Nilathak also have a rather high chance of dropping a rune, but not even close to the Countess. Nilathak can drop much higher runes though.
This guide might be helpful.
As for gems: Just go to areas with lots of monsters (cow level might be good) and collect all gems for transmuting.
Another option to farm runes and gems would be to do hellforge rushes. That's only viable online though where you can rush a lot of people at the same time and share the drops.
The Countess is the best rune dropper; she once dropped 4 runes for me! Usually it's 2, sometimes 3, seldom is it only one. The higher your clvl, the better the drops throughout the Tower, which will yield chipped gems or a chipped skull (1-2) ammys (1-2) a charm (0-1)and a ring (0-1). The Forgotten Tower is a farmer's delight!