What is a useful strategy to farm runes/gems in Diablo 2?

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.