Median XL contains the standard Diablo II runes with new bonuses, but also 30 new runes.
List of Runes
Fauztinville Great Runes
These three runes are very rare and can only be found in the Fauztinville uberon Destruction difficulty.
Toraja Great Runes
Secret Elemental Runes
On Destruction difficulty, in the Teganze uberlevel, you can come by Elemental Essences and Runestones.
You can cube them to get the Elemental Runes and Kabraxis' Stone rune: