Some of the answers here aren't very good. The one with the lowest rating is correct.
The Countess is not the best source of higher runes. To be fair, though, the OP didn't specify higher runes.
Some of the best ways to get runes:
- Play the game. Really, just play the character you like most in the highest level area that you can clear quickly. Look up the level 85 areas (e.g. The Pit in Act 1, The Ancient Tunnels in Act 2, The River of Flame in Act 4, the Worldstone Keep in Act 5) as they can drop any rune (or nearly any, my memory is fuzzy .... edit: champions and elites in those areas can drop any item in the game). The highest rune I've ever found on bnet was Sur in the WSK. The highest rune I've found in SP is Cham in The Glacial Trail (which has area level 83).
- Lower Kurast. This area has up to 6 "super chests," which have a decent chance to drop high(er) runes. The River of Flame is also a good area. It has a higher area level, so it can drop higher runes than LK, but it only has at most 2 such chests. In SP, /p7 is best for LK.
- Travincal. The council in Travincal have a decent chance to drop a lot of good items (runes, charms, jewelry, and facets, for example). One of the best features, though, is that the map is static. You always know exactly where the council will be when you join a game. For bnet, this is a big deal. In SP, /p3 is best.
- The Countess is a good way to get low to mid runes throughout Normal, Nightmare, and Hell. In Hell, though, she's really not that great as she can't drop the highest runes. Always (...after the first "quest" drop) run the Countess solo on bnet or on /players1 in SP. For reasons that I don't recall right now, her rune drop is best in a solo game.
Oh, btw, for gems, see option 1 up there. On SP, you can engage in Gem Shrine Farming. Basically, you run and rerun The Stony Field, The Dark Wood, and The Black Marsh looking for "Gem" Shrines. Carry some flawless gems with you but no other, lower gems, and when you find the gem shrine, hitting it will upgrade one of the gems in your inventory/backpack to a perfect gem. You can do this on bnet, but since the maps change with every new game, it's really not efficient.