It is said that the Secret Cow level is best place for finding runes, but that's not true. the best place is Forgotten Tower in Black Marsh in ACT I. Just kill the Countess in there and she will ALWAYS drop runes. and since patch 1.10 you can use the following cupe recepies to upgrade runes over Thul Rune. use these recepies to get runes Amn - Zod

3 Thul Runes + 1 Chipped Topaz = Amn Rune
3 Amn Runes + 1 Chipped Amethyst = Sol Rune
3 Sol Runes + 1 Chipped Sapphire = Shael Rune
3 Shael Runes + 1 Chipped Ruby = Dol Rune
3 Dol Runes + 1 Chipped Emerald = Hel Rune
3 Hel Runes + 1 Chipped Diamond = Io Rune
3 Io Runes + 1 Flawed Topaz = Lum Rune
3 Lum Runes + 1 Flawed Amethyst = Ko Rune
3 Ko Runes + 1 Flawed Sapphire = Fal Rune
3 Fal Runes + 1 Flawed Ruby = Lem Rune
3 Lem Runes + 1 Flawed Emerald = Pul Rune
2 Pul Runes + 1 Flawed Diamond = Um Rune
2 Um Runes + 1 Topaz = Mal Rune
2 Mal Runes + 1 Amethyst = Ist Rune
2 Ist Runes + 1 Sapphire = Gul Rune
2 Gul Runes + 1 Ruby = Vex Rune
2 Vex Runes + 1 Emerald = Ohm Rune
2 Ohm Runes + 1 Diamond = Lo Rune
2 Lo Runes + 1 Flawless Topaz = Sur Rune
2 Sur Runes + 1 Flawless Amethyst = Ber Rune
2 Ber Runes + 1 Flawless Sapphire = Jah Rune
2 Jah Runes + 1 Flawless Ruby = Cham Rune
2 Cham Runes + 1 Flawless Emerald = Zod Rune

This Doesn't Work on Battle.net!