Median XL contains the standard Diablo II runes with new bonuses, but also 30 new runes.
List of Runes
Fauztinville Great Runes
Toraja Great Runes
On Hell 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: